Changes between Initial Version and Version 1 of Ticket #17282


Ignore:
Timestamp:
Apr 7, 2025, 10:03:27 AM (7 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17282

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash closing dock widget

  • Ticket #17282 – Description

    initial v1  
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    715715  "faultingThread" : 0,
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     720
    2307721],
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    … …  
    28921306Associated chain_V chain V to chain V with 0 mismatches 
    28931307Associated chain_V chain W to chain V with 0 mismatches 
    2894 Chain information for chain_V 
    2895 --- 
    2896 Chain | Description 
    2897 5.1/V 5.2/V 5.3/V 5.4/V 5.5/V 5.1/W 5.2/W 5.3/W 5.4/W 5.5/W | No description available 
    2898  
    2899 Modeller job (ID NTSM7C6V9BWV2E8Z) finished 
    2900 Parameters 
    2901 --- 
    2902 Chain pairing | ss 
    2903 Alignment algorithm | Needleman-Wunsch 
    2904 Similarity matrix | BLOSUM-62 
    2905 SS fraction | 0.3 
    2906 Gap open (HH/SS/other) | 18/18/6 
    2907 Gap extend | 1 
    2908 SS matrix |  |  | H | S | O 
    2909 ---|---|---|--- 
    2910 H | 6 | -9 | -6 
    2911 S |  | 6 | -6 
    2912 O |  |  | 4 
    2913 Iteration cutoff | 2 
    2914  
    2915 Matchmaker chain_V, chain V (#3.5) with chain_V, chain V (#), sequence
    2916 alignment score = 615.7 
    2917 Matchmaker chain_V, chain W (#3.5) with chain_V, chain W (#), sequence
    2918 alignment score = 616.7 
    2919 RMSD between 229 pruned atom pairs is 0.069 angstroms; (across all 229 pairs:
    2920 0.069) 
    2921  
    2922 Parameters 
    2923 --- 
    2924 Chain pairing | ss 
    2925 Alignment algorithm | Needleman-Wunsch 
    2926 Similarity matrix | BLOSUM-62 
    2927 SS fraction | 0.3 
    2928 Gap open (HH/SS/other) | 18/18/6 
    2929 Gap extend | 1 
    2930 SS matrix |  |  | H | S | O 
    2931 ---|---|---|--- 
    2932 H | 6 | -9 | -6 
    2933 S |  | 6 | -6 
    2934 O |  |  | 4 
    2935 Iteration cutoff | 2 
    2936  
    2937 Matchmaker chain_V, chain V (#3.5) with chain_V, chain V (#), sequence
    2938 alignment score = 615.7 
    2939 Matchmaker chain_V, chain W (#3.5) with chain_V, chain W (#), sequence
    2940 alignment score = 616.7 
    2941 RMSD between 229 pruned atom pairs is 0.062 angstroms; (across all 229 pairs:
    2942 0.062) 
    2943  
    2944 Parameters 
    2945 --- 
    2946 Chain pairing | ss 
    2947 Alignment algorithm | Needleman-Wunsch 
    2948 Similarity matrix | BLOSUM-62 
    2949 SS fraction | 0.3 
    2950 Gap open (HH/SS/other) | 18/18/6 
    2951 Gap extend | 1 
    2952 SS matrix |  |  | H | S | O 
    2953 ---|---|---|--- 
    2954 H | 6 | -9 | -6 
    2955 S |  | 6 | -6 
    2956 O |  |  | 4 
    2957 Iteration cutoff | 2 
    2958  
    2959 Matchmaker chain_V, chain V (#3.5) with chain_V, chain V (#), sequence
    2960 alignment score = 615.7 
    2961 Matchmaker chain_V, chain W (#3.5) with chain_V, chain W (#), sequence
    2962 alignment score = 616.7 
    2963 RMSD between 229 pruned atom pairs is 0.071 angstroms; (across all 229 pairs:
    2964 0.071) 
    2965  
    2966 Parameters 
    2967 --- 
    2968 Chain pairing | ss 
    2969 Alignment algorithm | Needleman-Wunsch 
    2970 Similarity matrix | BLOSUM-62 
    2971 SS fraction | 0.3 
    2972 Gap open (HH/SS/other) | 18/18/6 
    2973 Gap extend | 1 
    2974 SS matrix |  |  | H | S | O 
    2975 ---|---|---|--- 
    2976 H | 6 | -9 | -6 
    2977 S |  | 6 | -6 
    2978 O |  |  | 4 
    2979 Iteration cutoff | 2 
    2980  
    2981 Matchmaker chain_V, chain V (#3.5) with chain_V, chain V (#), sequence
    2982 alignment score = 615.7 
    2983 Matchmaker chain_V, chain W (#3.5) with chain_V, chain W (#), sequence
    2984 alignment score = 616.7 
    2985 RMSD between 229 pruned atom pairs is 0.134 angstroms; (across all 229 pairs:
    2986 0.134) 
    2987  
    2988 Parameters 
    2989 --- 
    2990 Chain pairing | ss 
    2991 Alignment algorithm | Needleman-Wunsch 
    2992 Similarity matrix | BLOSUM-62 
    2993 SS fraction | 0.3 
    2994 Gap open (HH/SS/other) | 18/18/6 
    2995 Gap extend | 1 
    2996 SS matrix |  |  | H | S | O 
    2997 ---|---|---|--- 
    2998 H | 6 | -9 | -6 
    2999 S |  | 6 | -6 
    3000 O |  |  | 4 
    3001 Iteration cutoff | 2 
    3002  
    3003 Matchmaker chain_V, chain V (#3.5) with chain_V, chain V (#), sequence
    3004 alignment score = 615.7 
    3005 Matchmaker chain_V, chain W (#3.5) with chain_V, chain W (#), sequence
    3006 alignment score = 616.7 
    3007 RMSD between 229 pruned atom pairs is 0.048 angstroms; (across all 229 pairs:
    3008 0.048) 
    3009  
    3010 Associated chain_V chain V to chain W with 0 mismatches 
    3011 Associated chain_V chain W to chain W with 0 mismatches 
    3012 Associated chain_V chain V to chain W with 0 mismatches 
    3013 Associated chain_V chain W to chain W with 0 mismatches 
    3014 Associated chain_V chain V to chain W with 0 mismatches 
    3015 Associated chain_V chain W to chain W with 0 mismatches 
    3016 Associated chain_V chain V to chain W with 0 mismatches 
    3017 Associated chain_V chain W to chain W with 0 mismatches 
    3018 Associated chain_V chain V to chain W with 0 mismatches 
    3019 Associated chain_V chain W to chain W with 0 mismatches 
    3020 Associated chain_V chain V to chain V with 0 mismatches 
    3021 Associated chain_V chain W to chain V with 0 mismatches 
    3022 Associated chain_V chain V to chain V with 0 mismatches 
    3023 Associated chain_V chain W to chain V with 0 mismatches 
    3024 Associated chain_V chain V to chain V with 0 mismatches 
    3025 Associated chain_V chain W to chain V with 0 mismatches 
    3026 Associated chain_V chain V to chain V with 0 mismatches 
    3027 Associated chain_V chain W to chain V with 0 mismatches 
    3028 Associated chain_V chain V to chain V with 0 mismatches 
    3029 Associated chain_V chain W to chain V with 0 mismatches 
    3030 Chain information for chain_V 
    3031 --- 
    3032 Chain | Description 
    3033 6.1/V 6.2/V 6.3/V 6.4/V 6.5/V 6.1/W 6.2/W 6.3/W 6.4/W 6.5/W | No description available 
    3034  
    3035 Modeller job (ID EZZX7UU75XAU1R8O) finished 
    3036 Parameters 
    3037 --- 
    3038 Chain pairing | ss 
    3039 Alignment algorithm | Needleman-Wunsch 
    3040 Similarity matrix | BLOSUM-62 
    3041 SS fraction | 0.3 
    3042 Gap open (HH/SS/other) | 18/18/6 
    3043 Gap extend | 1 
    3044 SS matrix |  |  | H | S | O 
    3045 ---|---|---|--- 
    3046 H | 6 | -9 | -6 
    3047 S |  | 6 | -6 
    3048 O |  |  | 4 
    3049 Iteration cutoff | 2 
    3050  
    3051 Matchmaker chain_V, chain V (#3.3) with chain_V, chain V (#), sequence
    3052 alignment score = 613.3 
    3053 Matchmaker chain_V, chain W (#3.3) with chain_V, chain W (#), sequence
    3054 alignment score = 619.1 
    3055 RMSD between 229 pruned atom pairs is 0.084 angstroms; (across all 229 pairs:
    3056 0.084) 
    3057  
    3058 Parameters 
    3059 --- 
    3060 Chain pairing | ss 
    3061 Alignment algorithm | Needleman-Wunsch 
    3062 Similarity matrix | BLOSUM-62 
    3063 SS fraction | 0.3 
    3064 Gap open (HH/SS/other) | 18/18/6 
    3065 Gap extend | 1 
    3066 SS matrix |  |  | H | S | O 
    3067 ---|---|---|--- 
    3068 H | 6 | -9 | -6 
    3069 S |  | 6 | -6 
    3070 O |  |  | 4 
    3071 Iteration cutoff | 2 
    3072  
    3073 Matchmaker chain_V, chain V (#3.3) with chain_V, chain V (#), sequence
    3074 alignment score = 613.3 
    3075 Matchmaker chain_V, chain W (#3.3) with chain_V, chain W (#), sequence
    3076 alignment score = 619.1 
    3077 RMSD between 229 pruned atom pairs is 0.136 angstroms; (across all 229 pairs:
    3078 0.136) 
    3079  
    3080 Parameters 
    3081 --- 
    3082 Chain pairing | ss 
    3083 Alignment algorithm | Needleman-Wunsch 
    3084 Similarity matrix | BLOSUM-62 
    3085 SS fraction | 0.3 
    3086 Gap open (HH/SS/other) | 18/18/6 
    3087 Gap extend | 1 
    3088 SS matrix |  |  | H | S | O 
    3089 ---|---|---|--- 
    3090 H | 6 | -9 | -6 
    3091 S |  | 6 | -6 
    3092 O |  |  | 4 
    3093 Iteration cutoff | 2 
    3094  
    3095 Matchmaker chain_V, chain V (#3.3) with chain_V, chain V (#), sequence
    3096 alignment score = 613.3 
    3097 Matchmaker chain_V, chain W (#3.3) with chain_V, chain W (#), sequence
    3098 alignment score = 619.1 
    3099 RMSD between 229 pruned atom pairs is 0.135 angstroms; (across all 229 pairs:
    3100 0.135) 
    3101  
    3102 Parameters 
    3103 --- 
    3104 Chain pairing | ss 
    3105 Alignment algorithm | Needleman-Wunsch 
    3106 Similarity matrix | BLOSUM-62 
    3107 SS fraction | 0.3 
    3108 Gap open (HH/SS/other) | 18/18/6 
    3109 Gap extend | 1 
    3110 SS matrix |  |  | H | S | O 
    3111 ---|---|---|--- 
    3112 H | 6 | -9 | -6 
    3113 S |  | 6 | -6 
    3114 O |  |  | 4 
    3115 Iteration cutoff | 2 
    3116  
    3117 Matchmaker chain_V, chain V (#3.3) with chain_V, chain V (#), sequence
    3118 alignment score = 613.3 
    3119 Matchmaker chain_V, chain W (#3.3) with chain_V, chain W (#), sequence
    3120 alignment score = 619.1 
    3121 RMSD between 229 pruned atom pairs is 0.046 angstroms; (across all 229 pairs:
    3122 0.046) 
    3123  
    3124 Parameters 
    3125 --- 
    3126 Chain pairing | ss 
    3127 Alignment algorithm | Needleman-Wunsch 
    3128 Similarity matrix | BLOSUM-62 
    3129 SS fraction | 0.3 
    3130 Gap open (HH/SS/other) | 18/18/6 
    3131 Gap extend | 1 
    3132 SS matrix |  |  | H | S | O 
    3133 ---|---|---|--- 
    3134 H | 6 | -9 | -6 
    3135 S |  | 6 | -6 
    3136 O |  |  | 4 
    3137 Iteration cutoff | 2 
    3138  
    3139 Matchmaker chain_V, chain V (#3.3) with chain_V, chain V (#), sequence
    3140 alignment score = 613.3 
    3141 Matchmaker chain_V, chain W (#3.3) with chain_V, chain W (#), sequence
    3142 alignment score = 619.1 
    3143 RMSD between 229 pruned atom pairs is 0.117 angstroms; (across all 229 pairs:
    3144 0.117) 
    3145  
    3146 Associated chain_V chain V to chain W with 0 mismatches 
    3147 Associated chain_V chain W to chain W with 0 mismatches 
    3148 Associated chain_V chain V to chain W with 0 mismatches 
    3149 Associated chain_V chain W to chain W with 0 mismatches 
    3150 Associated chain_V chain V to chain W with 0 mismatches 
    3151 Associated chain_V chain W to chain W with 0 mismatches 
    3152 Associated chain_V chain V to chain W with 0 mismatches 
    3153 Associated chain_V chain W to chain W with 0 mismatches 
    3154 Associated chain_V chain V to chain W with 0 mismatches 
    3155 Associated chain_V chain W to chain W with 0 mismatches 
    3156 Associated chain_V chain V to chain V with 0 mismatches 
    3157 Associated chain_V chain W to chain V with 0 mismatches 
    3158 Associated chain_V chain V to chain V with 0 mismatches 
    3159 Associated chain_V chain W to chain V with 0 mismatches 
    3160 Associated chain_V chain V to chain V with 0 mismatches 
    3161 Associated chain_V chain W to chain V with 0 mismatches 
    3162 Associated chain_V chain V to chain V with 0 mismatches 
    3163 Associated chain_V chain W to chain V with 0 mismatches 
    3164 Associated chain_V chain V to chain V with 0 mismatches 
    3165 Associated chain_V chain W to chain V with 0 mismatches 
    3166 Chain information for chain_V 
    3167 --- 
    3168 Chain | Description 
    3169 7.1/V 7.2/V 7.3/V 7.4/V 7.5/V 7.1/W 7.2/W 7.3/W 7.4/W 7.5/W | No description available 
    3170  
    3171 Modeller job (ID PGMBJ87EFSOBN1EV) finished 
    3172 Parameters 
    3173 --- 
    3174 Chain pairing | ss 
    3175 Alignment algorithm | Needleman-Wunsch 
    3176 Similarity matrix | BLOSUM-62 
    3177 SS fraction | 0.3 
    3178 Gap open (HH/SS/other) | 18/18/6 
    3179 Gap extend | 1 
    3180 SS matrix |  |  | H | S | O 
    3181 ---|---|---|--- 
    3182 H | 6 | -9 | -6 
    3183 S |  | 6 | -6 
    3184 O |  |  | 4 
    3185 Iteration cutoff | 2 
    3186  
    3187 Matchmaker chain_V, chain V (#3.4) with chain_V, chain V (#), sequence
    3188 alignment score = 613.3 
    3189 Matchmaker chain_V, chain W (#3.4) with chain_V, chain W (#), sequence
    3190 alignment score = 616.7 
    3191 RMSD between 229 pruned atom pairs is 0.083 angstroms; (across all 229 pairs:
    3192 0.083) 
    3193  
    3194 Parameters 
    3195 --- 
    3196 Chain pairing | ss 
    3197 Alignment algorithm | Needleman-Wunsch 
    3198 Similarity matrix | BLOSUM-62 
    3199 SS fraction | 0.3 
    3200 Gap open (HH/SS/other) | 18/18/6 
    3201 Gap extend | 1 
    3202 SS matrix |  |  | H | S | O 
    3203 ---|---|---|--- 
    3204 H | 6 | -9 | -6 
    3205 S |  | 6 | -6 
    3206 O |  |  | 4 
    3207 Iteration cutoff | 2 
    3208  
    3209 Matchmaker chain_V, chain V (#3.4) with chain_V, chain V (#), sequence
    3210 alignment score = 613.3 
    3211 Matchmaker chain_V, chain W (#3.4) with chain_V, chain W (#), sequence
    3212 alignment score = 616.7 
    3213 RMSD between 229 pruned atom pairs is 0.096 angstroms; (across all 229 pairs:
    3214 0.096) 
    3215  
    3216 Parameters 
    3217 --- 
    3218 Chain pairing | ss 
    3219 Alignment algorithm | Needleman-Wunsch 
    3220 Similarity matrix | BLOSUM-62 
    3221 SS fraction | 0.3 
    3222 Gap open (HH/SS/other) | 18/18/6 
    3223 Gap extend | 1 
    3224 SS matrix |  |  | H | S | O 
    3225 ---|---|---|--- 
    3226 H | 6 | -9 | -6 
    3227 S |  | 6 | -6 
    3228 O |  |  | 4 
    3229 Iteration cutoff | 2 
    3230  
    3231 Matchmaker chain_V, chain V (#3.4) with chain_V, chain V (#), sequence
    3232 alignment score = 613.3 
    3233 Matchmaker chain_V, chain W (#3.4) with chain_V, chain W (#), sequence
    3234 alignment score = 616.7 
    3235 RMSD between 229 pruned atom pairs is 0.074 angstroms; (across all 229 pairs:
    3236 0.074) 
    3237  
    3238 Parameters 
    3239 --- 
    3240 Chain pairing | ss 
    3241 Alignment algorithm | Needleman-Wunsch 
    3242 Similarity matrix | BLOSUM-62 
    3243 SS fraction | 0.3 
    3244 Gap open (HH/SS/other) | 18/18/6 
    3245 Gap extend | 1 
    3246 SS matrix |  |  | H | S | O 
    3247 ---|---|---|--- 
    3248 H | 6 | -9 | -6 
    3249 S |  | 6 | -6 
    3250 O |  |  | 4 
    3251 Iteration cutoff | 2 
    3252  
    3253 Matchmaker chain_V, chain V (#3.4) with chain_V, chain V (#), sequence
    3254 alignment score = 613.3 
    3255 Matchmaker chain_V, chain W (#3.4) with chain_V, chain W (#), sequence
    3256 alignment score = 616.7 
    3257 RMSD between 229 pruned atom pairs is 0.074 angstroms; (across all 229 pairs:
    3258 0.074) 
    3259  
    3260 Parameters 
    3261 --- 
    3262 Chain pairing | ss 
    3263 Alignment algorithm | Needleman-Wunsch 
    3264 Similarity matrix | BLOSUM-62 
    3265 SS fraction | 0.3 
    3266 Gap open (HH/SS/other) | 18/18/6 
    3267 Gap extend | 1 
    3268 SS matrix |  |  | H | S | O 
    3269 ---|---|---|--- 
    3270 H | 6 | -9 | -6 
    3271 S |  | 6 | -6 
    3272 O |  |  | 4 
    3273 Iteration cutoff | 2 
    3274  
    3275 Matchmaker chain_V, chain V (#3.4) with chain_V, chain V (#), sequence
    3276 alignment score = 613.3 
    3277 Matchmaker chain_V, chain W (#3.4) with chain_V, chain W (#), sequence
    3278 alignment score = 616.7 
    3279 RMSD between 229 pruned atom pairs is 0.071 angstroms; (across all 229 pairs:
    3280 0.071) 
    3281  
    3282 Associated chain_V chain V to chain W with 0 mismatches 
    3283 Associated chain_V chain W to chain W with 0 mismatches 
    3284 Associated chain_V chain V to chain W with 0 mismatches 
    3285 Associated chain_V chain W to chain W with 0 mismatches 
    3286 Associated chain_V chain V to chain W with 0 mismatches 
    3287 Associated chain_V chain W to chain W with 0 mismatches 
    3288 Associated chain_V chain V to chain W with 0 mismatches 
    3289 Associated chain_V chain W to chain W with 0 mismatches 
    3290 Associated chain_V chain V to chain W with 0 mismatches 
    3291 Associated chain_V chain W to chain W with 0 mismatches 
    3292 Associated chain_V chain V to chain V with 0 mismatches 
    3293 Associated chain_V chain W to chain V with 0 mismatches 
    3294 Associated chain_V chain V to chain V with 0 mismatches 
    3295 Associated chain_V chain W to chain V with 0 mismatches 
    3296 Associated chain_V chain V to chain V with 0 mismatches 
    3297 Associated chain_V chain W to chain V with 0 mismatches 
    3298 Associated chain_V chain V to chain V with 0 mismatches 
    3299 Associated chain_V chain W to chain V with 0 mismatches 
    3300 Associated chain_V chain V to chain V with 0 mismatches 
    3301 Associated chain_V chain W to chain V with 0 mismatches 
    3302 Chain information for chain_V 
    3303 --- 
    3304 Chain | Description 
    3305 8.1/V 8.2/V 8.3/V 8.4/V 8.5/V 8.1/W 8.2/W 8.3/W 8.4/W 8.5/W | No description available 
    3306  
    3307 Modeller job (ID NGQOJZ3X89CG8314) finished 
    3308 Parameters 
    3309 --- 
    3310 Chain pairing | ss 
    3311 Alignment algorithm | Needleman-Wunsch 
    3312 Similarity matrix | BLOSUM-62 
    3313 SS fraction | 0.3 
    3314 Gap open (HH/SS/other) | 18/18/6 
    3315 Gap extend | 1 
    3316 SS matrix |  |  | H | S | O 
    3317 ---|---|---|--- 
    3318 H | 6 | -9 | -6 
    3319 S |  | 6 | -6 
    3320 O |  |  | 4 
    3321 Iteration cutoff | 2 
    3322  
    3323 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
    3324 sequence alignment score = 624.3 
    3325 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
    3326 sequence alignment score = 615.9 
    3327 RMSD between 217 pruned atom pairs is 0.096 angstroms; (across all 217 pairs:
    3328 0.096) 
    3329  
    3330 Parameters 
    3331 --- 
    3332 Chain pairing | ss 
    3333 Alignment algorithm | Needleman-Wunsch 
    3334 Similarity matrix | BLOSUM-62 
    3335 SS fraction | 0.3 
    3336 Gap open (HH/SS/other) | 18/18/6 
    3337 Gap extend | 1 
    3338 SS matrix |  |  | H | S | O 
    3339 ---|---|---|--- 
    3340 H | 6 | -9 | -6 
    3341 S |  | 6 | -6 
    3342 O |  |  | 4 
    3343 Iteration cutoff | 2 
    3344  
    3345 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
    3346 sequence alignment score = 624.3 
    3347 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
    3348 sequence alignment score = 612.9 
    3349 RMSD between 217 pruned atom pairs is 0.155 angstroms; (across all 217 pairs:
    3350 0.155) 
    3351  
    3352 Parameters 
    3353 --- 
    3354 Chain pairing | ss 
    3355 Alignment algorithm | Needleman-Wunsch 
    3356 Similarity matrix | BLOSUM-62 
    3357 SS fraction | 0.3 
    3358 Gap open (HH/SS/other) | 18/18/6 
    3359 Gap extend | 1 
    3360 SS matrix |  |  | H | S | O 
    3361 ---|---|---|--- 
    3362 H | 6 | -9 | -6 
    3363 S |  | 6 | -6 
    3364 O |  |  | 4 
    3365 Iteration cutoff | 2 
    3366  
    3367 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
    3368 sequence alignment score = 624.3 
    3369 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
    3370 sequence alignment score = 615.9 
    3371 RMSD between 217 pruned atom pairs is 0.184 angstroms; (across all 217 pairs:
    3372 0.184) 
    3373  
    3374 Parameters 
    3375 --- 
    3376 Chain pairing | ss 
    3377 Alignment algorithm | Needleman-Wunsch 
    3378 Similarity matrix | BLOSUM-62 
    3379 SS fraction | 0.3 
    3380 Gap open (HH/SS/other) | 18/18/6 
    3381 Gap extend | 1 
    3382 SS matrix |  |  | H | S | O 
    3383 ---|---|---|--- 
    3384 H | 6 | -9 | -6 
    3385 S |  | 6 | -6 
    3386 O |  |  | 4 
    3387 Iteration cutoff | 2 
    3388  
    3389 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
    3390 sequence alignment score = 624.3 
    3391 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
    3392 sequence alignment score = 615.9 
    3393 RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
    3394 0.100) 
    3395  
    3396 Parameters 
    3397 --- 
    3398 Chain pairing | ss 
    3399 Alignment algorithm | Needleman-Wunsch 
    3400 Similarity matrix | BLOSUM-62 
    3401 SS fraction | 0.3 
    3402 Gap open (HH/SS/other) | 18/18/6 
    3403 Gap extend | 1 
    3404 SS matrix |  |  | H | S | O 
    3405 ---|---|---|--- 
    3406 H | 6 | -9 | -6 
    3407 S |  | 6 | -6 
    3408 O |  |  | 4 
    3409 Iteration cutoff | 2 
    3410  
    3411 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
    3412 sequence alignment score = 624.3 
    3413 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
    3414 sequence alignment score = 612.9 
    3415 RMSD between 217 pruned atom pairs is 0.107 angstroms; (across all 217 pairs:
    3416 0.107) 
    3417  
    3418 Associated chain_V chain V to chain W with 0 mismatches 
    3419 Associated chain_V chain W to chain W with 0 mismatches 
    3420 Associated chain_V chain V to chain W with 0 mismatches 
    3421 Associated chain_V chain W to chain W with 0 mismatches 
    3422 Associated chain_V chain V to chain W with 0 mismatches 
    3423 Associated chain_V chain W to chain W with 0 mismatches 
    3424 Associated chain_V chain V to chain W with 0 mismatches 
    3425 Associated chain_V chain W to chain W with 0 mismatches 
    3426 Associated chain_V chain V to chain W with 0 mismatches 
    3427 Associated chain_V chain W to chain W with 0 mismatches 
    3428 Associated chain_V chain V to chain V with 0 mismatches 
    3429 Associated chain_V chain W to chain V with 0 mismatches 
    3430 Associated chain_V chain V to chain V with 0 mismatches 
    3431 Associated chain_V chain W to chain V with 0 mismatches 
    3432 Associated chain_V chain V to chain V with 0 mismatches 
    3433 Associated chain_V chain W to chain V with 0 mismatches 
    3434 Associated chain_V chain V to chain V with 0 mismatches 
    3435 Associated chain_V chain W to chain V with 0 mismatches 
    3436 Associated chain_V chain V to chain V with 0 mismatches 
    3437 Associated chain_V chain W to chain V with 0 mismatches 
    3438 Chain information for chain_V 
    3439 --- 
    3440 Chain | Description 
    3441 9.1/V 9.2/V 9.3/V 9.4/V 9.5/V 9.1/W 9.2/W 9.3/W 9.4/W 9.5/W | No description available 
    3442  
    3443 
    3444 > hide #7.4 models
    3445 
    3446 > show #7.4 models
    3447 
    3448 > hide #7.4 models
    3449 
    3450 > hide #3.3 models
    3451 
    3452 > hide #7.1 models
    3453 
    3454 > hide #7.2 models
    3455 
    3456 > hide #7.3 models
    3457 
    3458 > hide #7.5 models
    3459 
    3460 > hide #9.4 models
    3461 
    3462 > hide #3.5 models
    3463 
    3464 > hide #6.1 models
    3465 
    3466 > hide #6.4 models
    3467 
    3468 > hide #6.2 models
    3469 
    3470 > hide #6.5 models
    3471 
    3472 > close #5
    3473 
    3474 > close #6
    3475 
    3476 > close #7
    3477 
    3478 > close #8
    3479 
    3480 > close #9
    3481 
    3482 > close #4
    3483 
    3484 > close #3
    3485 
    3486 > ui tool show "Model Loops"
    3487 
    3488 > modeller refine 1/V:1:all-missing 1/W:1:all-missing numModels 5 fast false
    3489 > adjacentFlexible 1 protocol DOPE
    3490 
    3491 Webservices job id: BMHN1CLFCV2W70V9 
    3492 
    3493 > ui tool show "Model Loops"
    3494 
    3495 > modeller refine 1/V:1:internal-missing 1/W:1:internal-missing numModels 5
    3496 > fast false adjacentFlexible 1 protocol DOPE
    3497 
    3498 Webservices job id: E5ZLJVTF8X2N803X 
    3499 
    3500 > select clear
    3501 
    3502 Modeller job (ID E5ZLJVTF8X2N803X) finished 
    3503 Parameters 
    3504 --- 
    3505 Chain pairing | ss 
    3506 Alignment algorithm | Needleman-Wunsch 
    3507 Similarity matrix | BLOSUM-62 
    3508 SS fraction | 0.3 
    3509 Gap open (HH/SS/other) | 18/18/6 
    3510 Gap extend | 1 
    3511 SS matrix |  |  | H | S | O 
    3512 ---|---|---|--- 
    3513 H | 6 | -9 | -6 
    3514 S |  | 6 | -6 
    3515 O |  |  | 4 
    3516 Iteration cutoff | 2 
    3517  
    3518 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3519 sequence alignment score = 606.1 
    3520 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3521 sequence alignment score = 600.5 
    3522 RMSD between 217 pruned atom pairs is 0.065 angstroms; (across all 217 pairs:
    3523 0.065) 
    3524  
    3525 Parameters 
    3526 --- 
    3527 Chain pairing | ss 
    3528 Alignment algorithm | Needleman-Wunsch 
    3529 Similarity matrix | BLOSUM-62 
    3530 SS fraction | 0.3 
    3531 Gap open (HH/SS/other) | 18/18/6 
    3532 Gap extend | 1 
    3533 SS matrix |  |  | H | S | O 
    3534 ---|---|---|--- 
    3535 H | 6 | -9 | -6 
    3536 S |  | 6 | -6 
    3537 O |  |  | 4 
    3538 Iteration cutoff | 2 
    3539  
    3540 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3541 sequence alignment score = 606.1 
    3542 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3543 sequence alignment score = 600.5 
    3544 RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
    3545 0.100) 
    3546  
    3547 Parameters 
    3548 --- 
    3549 Chain pairing | ss 
    3550 Alignment algorithm | Needleman-Wunsch 
    3551 Similarity matrix | BLOSUM-62 
    3552 SS fraction | 0.3 
    3553 Gap open (HH/SS/other) | 18/18/6 
    3554 Gap extend | 1 
    3555 SS matrix |  |  | H | S | O 
    3556 ---|---|---|--- 
    3557 H | 6 | -9 | -6 
    3558 S |  | 6 | -6 
    3559 O |  |  | 4 
    3560 Iteration cutoff | 2 
    3561  
    3562 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3563 sequence alignment score = 606.1 
    3564 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3565 sequence alignment score = 600.5 
    3566 RMSD between 217 pruned atom pairs is 0.094 angstroms; (across all 217 pairs:
    3567 0.094) 
    3568  
    3569 Parameters 
    3570 --- 
    3571 Chain pairing | ss 
    3572 Alignment algorithm | Needleman-Wunsch 
    3573 Similarity matrix | BLOSUM-62 
    3574 SS fraction | 0.3 
    3575 Gap open (HH/SS/other) | 18/18/6 
    3576 Gap extend | 1 
    3577 SS matrix |  |  | H | S | O 
    3578 ---|---|---|--- 
    3579 H | 6 | -9 | -6 
    3580 S |  | 6 | -6 
    3581 O |  |  | 4 
    3582 Iteration cutoff | 2 
    3583  
    3584 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3585 sequence alignment score = 606.1 
    3586 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3587 sequence alignment score = 600.5 
    3588 RMSD between 217 pruned atom pairs is 0.060 angstroms; (across all 217 pairs:
    3589 0.060) 
    3590  
    3591 Parameters 
    3592 --- 
    3593 Chain pairing | ss 
    3594 Alignment algorithm | Needleman-Wunsch 
    3595 Similarity matrix | BLOSUM-62 
    3596 SS fraction | 0.3 
    3597 Gap open (HH/SS/other) | 18/18/6 
    3598 Gap extend | 1 
    3599 SS matrix |  |  | H | S | O 
    3600 ---|---|---|--- 
    3601 H | 6 | -9 | -6 
    3602 S |  | 6 | -6 
    3603 O |  |  | 4 
    3604 Iteration cutoff | 2 
    3605  
    3606 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3607 sequence alignment score = 606.1 
    3608 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3609 sequence alignment score = 600.5 
    3610 RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
    3611 0.087) 
    3612  
    3613 Associated chain_W chain W to chain V with 0 mismatches 
    3614 Associated chain_W chain V to chain V with 0 mismatches 
    3615 Associated chain_W chain W to chain V with 0 mismatches 
    3616 Associated chain_W chain V to chain V with 0 mismatches 
    3617 Associated chain_W chain W to chain V with 0 mismatches 
    3618 Associated chain_W chain V to chain V with 0 mismatches 
    3619 Associated chain_W chain W to chain V with 0 mismatches 
    3620 Associated chain_W chain V to chain V with 0 mismatches 
    3621 Associated chain_W chain W to chain V with 0 mismatches 
    3622 Associated chain_W chain V to chain V with 0 mismatches 
    3623 Associated chain_W chain W to chain W with 0 mismatches 
    3624 Associated chain_W chain V to chain W with 0 mismatches 
    3625 Associated chain_W chain W to chain W with 0 mismatches 
    3626 Associated chain_W chain V to chain W with 0 mismatches 
    3627 Associated chain_W chain W to chain W with 0 mismatches 
    3628 Associated chain_W chain V to chain W with 0 mismatches 
    3629 Associated chain_W chain W to chain W with 0 mismatches 
    3630 Associated chain_W chain V to chain W with 0 mismatches 
    3631 Associated chain_W chain W to chain W with 0 mismatches 
    3632 Associated chain_W chain V to chain W with 0 mismatches 
    3633 Chain information for chain_W 
    3634 --- 
    3635 Chain | Description 
    3636 3.1/V 3.2/V 3.3/V 3.4/V 3.5/V | No description available 
    3637 3.1/W 3.2/W 3.3/W 3.4/W 3.5/W | No description available 
    3638  
    3639 
    3640 > select #3.1/V:61-66/W:181-186,236 #3.2/V:61-66/W:181-186,236
    3641 > #3.3/V:61-66/W:181-186,236 #3.4/V:61-66/W:181-186,236
    3642 > #3.5/V:61-66/W:181-186,236 #1/W:236
    3643 
    3644 470 atoms, 474 bonds, 66 residues, 6 models selected 
    3645 
    3646 > hide #3.3 models
    3647 
    3648 > hide #3.5 models
    3649 
    3650 > hide #3.1 models
    3651 
    3652 Modeller job (ID BMHN1CLFCV2W70V9) finished 
    3653 Parameters 
    3654 --- 
    3655 Chain pairing | ss 
    3656 Alignment algorithm | Needleman-Wunsch 
    3657 Similarity matrix | BLOSUM-62 
    3658 SS fraction | 0.3 
    3659 Gap open (HH/SS/other) | 18/18/6 
    3660 Gap extend | 1 
    3661 SS matrix |  |  | H | S | O 
    3662 ---|---|---|--- 
    3663 H | 6 | -9 | -6 
    3664 S |  | 6 | -6 
    3665 O |  |  | 4 
    3666 Iteration cutoff | 2 
    3667  
    3668 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3669 sequence alignment score = 624.3 
    3670 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3671 sequence alignment score = 615.9 
    3672 RMSD between 217 pruned atom pairs is 0.096 angstroms; (across all 217 pairs:
    3673 0.096) 
    3674  
    3675 Parameters 
    3676 --- 
    3677 Chain pairing | ss 
    3678 Alignment algorithm | Needleman-Wunsch 
    3679 Similarity matrix | BLOSUM-62 
    3680 SS fraction | 0.3 
    3681 Gap open (HH/SS/other) | 18/18/6 
    3682 Gap extend | 1 
    3683 SS matrix |  |  | H | S | O 
    3684 ---|---|---|--- 
    3685 H | 6 | -9 | -6 
    3686 S |  | 6 | -6 
    3687 O |  |  | 4 
    3688 Iteration cutoff | 2 
    3689  
    3690 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3691 sequence alignment score = 624.3 
    3692 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3693 sequence alignment score = 612.9 
    3694 RMSD between 217 pruned atom pairs is 0.155 angstroms; (across all 217 pairs:
    3695 0.155) 
    3696  
    3697 Parameters 
    3698 --- 
    3699 Chain pairing | ss 
    3700 Alignment algorithm | Needleman-Wunsch 
    3701 Similarity matrix | BLOSUM-62 
    3702 SS fraction | 0.3 
    3703 Gap open (HH/SS/other) | 18/18/6 
    3704 Gap extend | 1 
    3705 SS matrix |  |  | H | S | O 
    3706 ---|---|---|--- 
    3707 H | 6 | -9 | -6 
    3708 S |  | 6 | -6 
    3709 O |  |  | 4 
    3710 Iteration cutoff | 2 
    3711  
    3712 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3713 sequence alignment score = 624.3 
    3714 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3715 sequence alignment score = 615.9 
    3716 RMSD between 217 pruned atom pairs is 0.184 angstroms; (across all 217 pairs:
    3717 0.184) 
    3718  
    3719 Parameters 
    3720 --- 
    3721 Chain pairing | ss 
    3722 Alignment algorithm | Needleman-Wunsch 
    3723 Similarity matrix | BLOSUM-62 
    3724 SS fraction | 0.3 
    3725 Gap open (HH/SS/other) | 18/18/6 
    3726 Gap extend | 1 
    3727 SS matrix |  |  | H | S | O 
    3728 ---|---|---|--- 
    3729 H | 6 | -9 | -6 
    3730 S |  | 6 | -6 
    3731 O |  |  | 4 
    3732 Iteration cutoff | 2 
    3733  
    3734 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3735 sequence alignment score = 624.3 
    3736 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3737 sequence alignment score = 615.9 
    3738 RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
    3739 0.100) 
    3740  
    3741 Parameters 
    3742 --- 
    3743 Chain pairing | ss 
    3744 Alignment algorithm | Needleman-Wunsch 
    3745 Similarity matrix | BLOSUM-62 
    3746 SS fraction | 0.3 
    3747 Gap open (HH/SS/other) | 18/18/6 
    3748 Gap extend | 1 
    3749 SS matrix |  |  | H | S | O 
    3750 ---|---|---|--- 
    3751 H | 6 | -9 | -6 
    3752 S |  | 6 | -6 
    3753 O |  |  | 4 
    3754 Iteration cutoff | 2 
    3755  
    3756 Matchmaker 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
    3757 sequence alignment score = 624.3 
    3758 Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
    3759 sequence alignment score = 612.9 
    3760 RMSD between 217 pruned atom pairs is 0.107 angstroms; (across all 217 pairs:
    3761 0.107) 
    3762  
    3763 Associated chain_W chain V to chain V with 0 mismatches 
    3764 Associated chain_W chain W to chain V with 0 mismatches 
    3765 Associated chain_W chain V to chain V with 0 mismatches 
    3766 Associated chain_W chain W to chain V with 0 mismatches 
    3767 Associated chain_W chain V to chain V with 0 mismatches 
    3768 Associated chain_W chain W to chain V with 0 mismatches 
    3769 Associated chain_W chain V to chain V with 0 mismatches 
    3770 Associated chain_W chain W to chain V with 0 mismatches 
    3771 Associated chain_W chain V to chain V with 0 mismatches 
    3772 Associated chain_W chain W to chain V with 0 mismatches 
    3773 Associated chain_W chain V to chain W with 0 mismatches 
    3774 Associated chain_W chain W to chain W with 0 mismatches 
    3775 Associated chain_W chain V to chain W with 0 mismatches 
    3776 Associated chain_W chain W to chain W with 0 mismatches 
    3777 Associated chain_W chain V to chain W with 0 mismatches 
    3778 Associated chain_W chain W to chain W with 0 mismatches 
    3779 Associated chain_W chain V to chain W with 0 mismatches 
    3780 Associated chain_W chain W to chain W with 0 mismatches 
    3781 Associated chain_W chain V to chain W with 0 mismatches 
    3782 Associated chain_W chain W to chain W with 0 mismatches 
    3783 Chain information for chain_W 
    3784 --- 
    3785 Chain | Description 
    3786 4.1/V 4.2/V 4.3/V 4.4/V 4.5/V 4.1/W 4.2/W 4.3/W 4.4/W 4.5/W | No description available 
    3787  
    3788 
    3789 > close #4
    3790 
    3791 > hide #3.2 models
    3792 
    3793 > hide #3.4 models
    3794 
    3795 > show #3.3 models
    3796 
    3797 > hide #3.3 models
    3798 
    3799 > show #3.2 models
    3800 
    3801 > hide #3.2 models
    3802 
    3803 > show #3.2 models
    3804 
    3805 > hide #3.2 models
    3806 
    3807 > show #3.3 models
    3808 
    3809 > hide #3.3 models
    3810 
    3811 > ui tool show "Model Loops"
    3812 
    3813 > modeller refine 1/V:1:internal-missing 1/W:1:internal-missing numModels 10
    3814 > fast false adjacentFlexible 1 protocol DOPE
    3815 
    3816 Webservices job id: 3RE2I7008A4AJVGV 
    3817 Webservices job id: 3JNS8SC6YQ67NIYB 
    3818 Webservices job id: 4N4DRLUWRS52AZE2 
    3819 Webservices job id: 8EF664GPC52WVSQB 
    3820 Webservices job id: 9768OIBIUKACZK45 
    3821 Webservices job id: LTL1YE68ZN1VUUVV 
    3822 Modeller job (ID 3RE2I7008A4AJVGV) finished 
    3823  
    3824 Modeller error output 
    3825 Traceback (most recent call last): 
    3826 File "ModellerModelling.py", line 93, in   
    3827 a.make() 
    3828 File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
    3829 line 42, in make 
    3830 AutoModel.make(self, exit_stage) 
    3831 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    3832 line 151, in make 
    3833 atmsel = self._check_select_atoms() 
    3834 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    3835 line 700, in _check_select_atoms 
    3836 raise ModellerError("no atoms selected for optimization") 
    3837 _modeller.ModellerError: no atoms selected for optimization 
    3838  
    3839  
    3840 Modeller run output 
    3841  
    3842 MODELLER 10.6, 2024/10/17, r12888 
    3843  
    3844 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    3845  
    3846  
    3847 Copyright(c) 1989-2024 Andrej Sali 
    3848 All Rights Reserved 
    3849  
    3850 Written by A. Sali 
    3851 with help from 
    3852 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    3853 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    3854 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    3855 F. Melo, J.P. Overington, E. Feyfant 
    3856 University of California, San Francisco, USA 
    3857 Rockefeller University, New York, USA 
    3858 Harvard University, Cambridge, USA 
    3859 Imperial Cancer Research Fund, London, UK 
    3860 Birkbeck College, University of London, London, UK 
    3861  
    3862  
    3863 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    3864 4.18.0-553.44.1.el8_10.x86_64 x86_64 
    3865 Date and time of compilation : 2024/10/17 20:43:03 
    3866 MODELLER executable type : x86_64-intel8 
    3867 Job starting time (YY/MM/DD HH:MM:SS): 2025/04/03 10:33:44 
    3868  
    3869 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    3870 openf___224_> Open $(LIB)/restyp.lib 
    3871 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    3872 rdresgr_266_> Number of residue groups: 2 
    3873 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    3874  
    3875 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    3876 0.183 
    3877  
    3878 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    3879 0.183 
    3880 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    3881  
    3882 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    3883 0.230 
    3884 rdrdih__263_> Number of dihedral angle types : 9 
    3885 Maximal number of dihedral angle optima: 3 
    3886 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    3887 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    3888  
    3889 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    3890 0.242 
    3891 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    3892 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    3893 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    3894 rdclass_257_> Number of classes: 5 
    3895 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    3896 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    3897 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    3898 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    3899 rdrrwgh_268_> Number of residue types: 21 
    3900 dope_loopm_W> The class 'dope_loopmodel' is deprecated; use 'DOPELoopModel'
    3901 instead 
    3902 openf___224_> Open alignment.ali 
    3903  
    3904 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
    3905 0.270 
    3906  
    3907 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
    3908 0.284 
    3909  
    3910 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
    3911 0.299 
    3912  
    3913 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
    3914 0.328 
    3915  
    3916 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
    3917 0.387 
    3918  
    3919 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405537 396.032 0.387 
    3920  
    3921 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405565 396.060 0.387 
    3922  
    3923 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406477 396.950 0.388 
    3924  
    3925 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407389 397.841 0.389 
    3926  
    3927 Read the alignment from file : alignment.ali 
    3928  
    3929 Total number of alignment positions: 229 
    3930  
    3931 # Code #_Res #_Segm PDB_code Name 
    3932 \------------------------------------------------------------------------------- 
    3933 1 chain_W_3 229 2 chain_W_3.5 
    3934 2 chain_W 229 2 chain_W 
    3935 check_a_343_> >> BEGINNING OF COMMAND 
    3936 openf___224_> Open ./chain_W_3.5.pdb 
    3937  
    3938 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477814 466.615
    3939 0.456 
    3940  
    3941 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 477814 466.615 0.456 
    3942  
    3943 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477985 466.782
    3944 0.456 
    3945  
    3946 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478835 467.612
    3947 0.457 
    3948  
    3949 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480093 468.841
    3950 0.458 
    3951  
    3952 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481997 470.700
    3953 0.460 
    3954  
    3955 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481997 470.700 0.460 
    3956  
    3957 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482087 470.788
    3958 0.460 
    3959  
    3960 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 484943 473.577
    3961 0.462 
    3962  
    3963 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 484943 473.577 0.462 
    3964  
    3965 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485078 473.709
    3966 0.463 
    3967  
    3968 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489362 477.893
    3969 0.467 
    3970  
    3971 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489362 477.893 0.467 
    3972  
    3973 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489560 478.086
    3974 0.467 
    3975  
    3976 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495986 484.361
    3977 0.473 
    3978  
    3979 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495986 484.361 0.473 
    3980  
    3981 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496283 484.651
    3982 0.473 
    3983  
    3984 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505905 494.048
    3985 0.482 
    3986  
    3987 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505905 494.048 0.482 
    3988  
    3989 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506355 494.487
    3990 0.483 
    3991  
    3992 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    3993 0.497 
    3994  
    3995 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    3996  
    3997 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    3998 0.497 
    3999  
    4000 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    4001  
    4002 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521480 509.258
    4003 0.497 
    4004  
    4005 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543138 530.408
    4006 0.518 
    4007  
    4008 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543138 530.408 0.518 
    4009  
    4010 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 544146 531.393
    4011 0.519 
    4012  
    4013 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543174 530.443
    4014 0.518 
    4015  
    4016 check_ali___> Checking the sequence-structure alignment. 
    4017  
    4018 Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: 
    4019  
    4020 ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST 
    4021 \---------------------------------------------- 
    4022 END OF TABLE 
    4023 check_a_344_>  Open ${LIB}/top_heav.lib 
    4024 read_to_681_> topology.submodel read from topology file: 3 
    4025 openf___224_> Open ${LIB}/par.lib 
    4026  
    4027 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682426 666.432
    4028 0.651 
    4029  
    4030 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 684026 667.994
    4031 0.652 
    4032  
    4033 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688006 671.881
    4034 0.656 
    4035  
    4036 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690006 673.834
    4037 0.658 
    4038  
    4039 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693006 676.764
    4040 0.661 
    4041  
    4042 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 697506 681.158
    4043 0.665 
    4044  
    4045 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703078 686.600
    4046 0.671 
    4047  
    4048 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705878 689.334
    4049 0.673 
    4050  
    4051 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710078 693.436
    4052 0.677 
    4053  
    4054 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 716378 699.588
    4055 0.683 
    4056  
    4057 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719150 702.295
    4058 0.686 
    4059  
    4060 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720550 703.662
    4061 0.687 
    4062 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 
    4063 227 561 661 112 0 
    4064  
    4065 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 738291 720.987 0.704 
    4066  
    4067 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 828353 808.938 0.790 
    4068  
    4069 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 841945 822.212 0.803 
    4070  
    4071 mkilst______> segment topology constructed from sequence and RTF: 
    4072 segments residues atoms bonds angles dihedrals impropers: 
    4073 1 114 900 921 0 0 389 
    4074  
    4075 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 880665 860.024 0.840 
    4076  
    4077 patch_______> segment topology patched using RTF: 1 ; SER ; NTER 
    4078 segments residues atoms bonds angles dihedrals impropers: 
    4079 1 114 900 921 1245 1488 389 
    4080  
    4081  
    4082 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 917761 896.251 0.875 
    4083 patch_______> segment topology patched using RTF: 114 ; LYS ; CTER 
    4084 segments residues atoms bonds angles dihedrals impropers: 
    4085 1 114 901 922 1247 1490 390 
    4086  
    4087 genseg______> segment topology constructed from sequence and RTF: 
    4088 segments residues atoms bonds angles dihedrals impropers: 
    4089 1 114 901 922 1247 1490 390 
    4090  
    4091 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 917789 896.278 0.875 
    4092  
    4093 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 935844 913.910 0.892 
    4094  
    4095 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1024632 1000.617 0.977 
    4096  
    4097 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1038320 1013.984 0.990 
    4098  
    4099 mkilst______> segment topology constructed from sequence and RTF: 
    4100 segments residues atoms bonds angles dihedrals impropers: 
    4101 2 229 1806 1848 1247 1490 781 
    4102  
    4103 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1077280 1052.031 1.027 
    4104  
    4105 patch_______> segment topology patched using RTF: 115 ; SER ; NTER 
    4106 segments residues atoms bonds angles dihedrals impropers: 
    4107 2 229 1806 1848 2499 2986 781 
    4108  
    4109  
    4110 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117016 1090.836 1.065 
    4111 patch_______> segment topology patched using RTF: 229 ; ALA ; CTER 
    4112 segments residues atoms bonds angles dihedrals impropers: 
    4113 2 229 1807 1849 2501 2988 782 
    4114  
    4115 genseg______> segment topology constructed from sequence and RTF: 
    4116 segments residues atoms bonds angles dihedrals impropers: 
    4117 2 229 1807 1849 2501 2988 782 
    4118  
    4119 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135520 1108.906 1.083 
    4120 patch_______> segment topology patched using RTF: 14 79 ; CYS CYS ; DISU 
    4121 segments residues atoms bonds angles dihedrals impropers: 
    4122 2 229 1807 1850 2503 2991 782 
    4123 patch_______> segment topology patched using RTF: 57 107 ; CYS CYS ; DISU 
    4124 segments residues atoms bonds angles dihedrals impropers: 
    4125 2 229 1807 1851 2505 2994 782 
    4126  
    4127 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135768 1109.148 1.083 
    4128 patch_______> segment topology patched using RTF: 67 109 ; CYS CYS ; DISU 
    4129 segments residues atoms bonds angles dihedrals impropers: 
    4130 2 229 1807 1852 2507 2997 782 
    4131 patch_______> segment topology patched using RTF: 128 193 ; CYS CYS ; DISU 
    4132 segments residues atoms bonds angles dihedrals impropers: 
    4133 2 229 1807 1853 2509 3000 782 
    4134 patch_______> segment topology patched using RTF: 171 221 ; CYS CYS ; DISU 
    4135 segments residues atoms bonds angles dihedrals impropers: 
    4136 2 229 1807 1854 2511 3003 782 
    4137 patch_______> segment topology patched using RTF: 181 223 ; CYS CYS ; DISU 
    4138 segments residues atoms bonds angles dihedrals impropers: 
    4139 2 229 1807 1855 2513 3006 782 
    4140 patch_s_522_> Number of disulfides patched in MODEL: 6 
    4141 transfe_506_> MODEL is an average of all templates. 
    4142 transfe_511_> Number of templates for coordinate transfer: 1 
    4143 After transferring coordinates of the equivalent template atoms, 
    4144 there are defined, undefined atoms in MODEL: 1807 0 
    4145 openf___224_> Open chain_W.ini 
    4146 wrpdb___568_> Residues, atoms, selected atoms: 229 1807 1807 
    4147 make_re_417_> Restraint type to be calculated: stereo 
    4148  
    4149 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1243217 1214.079
    4150 1.186 
    4151  
    4152 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251409 1222.079
    4153 1.193 
    4154  
    4155 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1267793 1238.079
    4156 1.209 
    4157  
    4158 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300561 1270.079
    4159 1.240 
    4160  
    4161 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1333329 1302.079
    4162 1.272 
    4163  
    4164 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398865 1366.079
    4165 1.334 
    4166  
    4167 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431633 1398.079
    4168 1.365 
    4169  
    4170 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1464401 1430.079
    4171 1.397 
    4172  
    4173 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529937 1494.079
    4174 1.459 
    4175  
    4176 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661009 1622.079
    4177 1.584 
    4178  
    4179 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1726545 1686.079
    4180 1.647 
    4181 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. 
    4182 Added bond,angle,dihedral,improper restraints : 1855 2513 2847 776 
    4183 Total number of restraints before, now : 0 7991 
    4184 make_re_422_> Number of previous, current restraints : 0 7991 
    4185 make_re_423_> Number of previous, current selected restraints: 0 7991 
    4186 make_re_417_> Restraint type to be calculated: phi-psi_binormal 
    4187  
    4188 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1857779 1814.237
    4189 1.772 
    4190 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin 
    4191 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt 
    4192 getdata_643_> Protein accepted: chain_W_3.5 
    4193 getdata_289_> Proteins (all/accepted): 1 1 
    4194  
    4195 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923331 1878.253
    4196 1.834 
    4197  
    4198 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054403 2006.253
    4199 1.959 
    4200 make_re_422_> Number of previous, current restraints : 7991 8216 
    4201 make_re_423_> Number of previous, current selected restraints: 7991 8216 
    4202 make_re_417_> Restraint type to be calculated: omega_dihedral 
    4203  
    4204 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4205 1.959 
    4206 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin 
    4207 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt 
    4208 getdata_643_> Protein accepted: chain_W_3.5 
    4209 getdata_289_> Proteins (all/accepted): 1 1 
    4210 omgdel__425_> Unselected all O C +N +CA dihedrals: 233 
    4211 (This is to avoid clashes between STEREO 
    4212 and OMEGA_DIHEDRAL restraints) 
    4213 make_re_422_> Number of previous, current restraints : 8216 8443 
    4214 make_re_423_> Number of previous, current selected restraints: 8216 8210 
    4215 make_re_417_> Restraint type to be calculated: chi1_dihedral 
    4216  
    4217 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4218 1.959 
    4219 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4220 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt 
    4221 getdata_643_> Protein accepted: chain_W_3.5 
    4222 getdata_289_> Proteins (all/accepted): 1 1 
    4223 make_re_422_> Number of previous, current restraints : 8443 8647 
    4224 make_re_423_> Number of previous, current selected restraints: 8210 8414 
    4225 make_re_417_> Restraint type to be calculated: chi2_dihedral 
    4226  
    4227 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4228 1.959 
    4229 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4230 openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt 
    4231 getdata_643_> Protein accepted: chain_W_3.5 
    4232 getdata_289_> Proteins (all/accepted): 1 1 
    4233  
    4234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185475 2134.253
    4235 2.084 
    4236 make_re_422_> Number of previous, current restraints : 8647 8775 
    4237 make_re_423_> Number of previous, current selected restraints: 8414 8542 
    4238 make_re_417_> Restraint type to be calculated: chi3_dihedral 
    4239  
    4240 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    4241 2.084 
    4242 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4243 openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt 
    4244 getdata_643_> Protein accepted: chain_W_3.5 
    4245 getdata_289_> Proteins (all/accepted): 1 1 
    4246 make_re_422_> Number of previous, current restraints : 8775 8827 
    4247 make_re_423_> Number of previous, current selected restraints: 8542 8594 
    4248 make_re_417_> Restraint type to be calculated: chi4_dihedral 
    4249  
    4250 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    4251 2.084 
    4252 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4253 openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt 
    4254 mdtrsr__446W> A potential that relies on one protein is used, yet you have at 
    4255 least one known structure available. MDT, not library, potential is used. 
    4256 getdata_643_> Protein accepted: chain_W_3.5 
    4257 getdata_289_> Proteins (all/accepted): 1 1 
    4258 make_re_422_> Number of previous, current restraints : 8827 8857 
    4259 make_re_423_> Number of previous, current selected restraints: 8594 8624 
    4260 make_re_417_> Restraint type to be calculated: DISTANCE 
    4261  
    4262 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2705855 2642.437
    4263 2.581 
    4264  
    4265 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2967999 2898.437
    4266 2.831 
    4267  
    4268 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3099071 3026.437
    4269 2.956 
    4270 make_re_422_> Number of previous, current restraints : 8857 13025 
    4271 make_re_423_> Number of previous, current selected restraints: 8624 12792 
    4272 make_re_417_> Restraint type to be calculated: DISTANCE 
    4273  
    4274 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3361215 3282.437
    4275 3.206 
    4276 make_re_422_> Number of previous, current restraints : 13025 17487 
    4277 make_re_423_> Number of previous, current selected restraints: 12792 17254 
    4278 make_re_417_> Restraint type to be calculated: DISTANCE 
    4279  
    4280 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3885503 3794.437
    4281 3.706 
    4282 make_re_422_> Number of previous, current restraints : 17487 21544 
    4283 make_re_423_> Number of previous, current selected restraints: 17254 21311 
    4284 make_re_417_> Restraint type to be calculated: DISTANCE 
    4285  
    4286 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4147647 4050.437
    4287 3.956 
    4288 make_re_422_> Number of previous, current restraints : 21544 23510 
    4289 make_re_423_> Number of previous, current selected restraints: 21311 23277 
    4290 0 atoms in HETATM/BLK residues constrained 
    4291 to protein atoms within 2.30 angstroms 
    4292 and protein CA atoms within 10.00 angstroms 
    4293 make_re_417_> Restraint type to be calculated: DISTANCE 
    4294 make_re_422_> Number of previous, current restraints : 23510 23510 
    4295 make_re_423_> Number of previous, current selected restraints: 23277 23277 
    4296 make_re_417_> Restraint type to be calculated: DISTANCE 
    4297 make_re_422_> Number of previous, current restraints : 23510 23510 
    4298 make_re_423_> Number of previous, current selected restraints: 23277 23277 
    4299 make_re_417_> Restraint type to be calculated: DISTANCE 
    4300 make_re_422_> Number of previous, current restraints : 23510 23510 
    4301 make_re_423_> Number of previous, current selected restraints: 23277 23277 
    4302 make_re_417_> Restraint type to be calculated: DISTANCE 
    4303 make_re_422_> Number of previous, current restraints : 23510 23510 
    4304 make_re_423_> Number of previous, current selected restraints: 23277 23277 
    4305 0 atoms in residues without defined topology 
    4306 constrained to be rigid bodies 
    4307 make_re_417_> Restraint type to be calculated: DISTANCE 
    4308 make_re_422_> Number of previous, current restraints : 23510 23510 
    4309 make_re_423_> Number of previous, current selected restraints: 23277 23277 
    4310 rmdupl__427_> 1360 redundant cosine dihedral restraints were unselected. 
    4311 condens_443_> Restraints marked for deletion were removed. 
    4312 Total number of restraints before, now: 23510 21917 
    4313 openf___224_> Open chain_W.rsr 
    4314 openf___224_> Open chain_W.rsr 
    4315  
    4316 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4260279 4160.429
    4317 4.063 
    4318 rdcsr2__307_> Number of restraints read : 21917 
    4319 Number of excluded pairs read: 0 
    4320 Number of pseudo atoms read : 0 
    4321 rdcsrs__304_> Restraints in memory, selected restraints: 21917 21917 
    4322 Explicitly excluded atom pairs in memory : 0 
    4323 Pseudo atoms in memory : 0 
    4324  
    4325 No output models from Modeller; see log for Modeller text output. 
    4326 Modeller job (ID 3JNS8SC6YQ67NIYB) finished 
    4327  
    4328 Modeller error output 
    4329 Traceback (most recent call last): 
    4330 File "ModellerModelling.py", line 93, in   
    4331 a.make() 
    4332 File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
    4333 line 42, in make 
    4334 AutoModel.make(self, exit_stage) 
    4335 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    4336 line 151, in make 
    4337 atmsel = self._check_select_atoms() 
    4338 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    4339 line 700, in _check_select_atoms 
    4340 raise ModellerError("no atoms selected for optimization") 
    4341 _modeller.ModellerError: no atoms selected for optimization 
    4342  
    4343  
    4344 Modeller run output 
    4345  
    4346 MODELLER 10.6, 2024/10/17, r12888 
    4347  
    4348 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    4349  
    4350  
    4351 Copyright(c) 1989-2024 Andrej Sali 
    4352 All Rights Reserved 
    4353  
    4354 Written by A. Sali 
    4355 with help from 
    4356 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    4357 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    4358 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    4359 F. Melo, J.P. Overington, E. Feyfant 
    4360 University of California, San Francisco, USA 
    4361 Rockefeller University, New York, USA 
    4362 Harvard University, Cambridge, USA 
    4363 Imperial Cancer Research Fund, London, UK 
    4364 Birkbeck College, University of London, London, UK 
    4365  
    4366  
    4367 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    4368 4.18.0-553.44.1.el8_10.x86_64 x86_64 
    4369 Date and time of compilation : 2024/10/17 20:43:03 
    4370 MODELLER executable type : x86_64-intel8 
    4371 Job starting time (YY/MM/DD HH:MM:SS): 2025/04/03 10:33:44 
    4372  
    4373 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    4374 openf___224_> Open $(LIB)/restyp.lib 
    4375 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    4376 rdresgr_266_> Number of residue groups: 2 
    4377 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    4378  
    4379 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    4380 0.183 
    4381  
    4382 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    4383 0.183 
    4384 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    4385  
    4386 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    4387 0.230 
    4388 rdrdih__263_> Number of dihedral angle types : 9 
    4389 Maximal number of dihedral angle optima: 3 
    4390 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    4391 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    4392  
    4393 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    4394 0.242 
    4395 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    4396 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    4397 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    4398 rdclass_257_> Number of classes: 5 
    4399 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    4400 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    4401 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    4402 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    4403 rdrrwgh_268_> Number of residue types: 21 
    4404 dope_loopm_W> The class 'dope_loopmodel' is deprecated; use 'DOPELoopModel'
    4405 instead 
    4406 openf___224_> Open alignment.ali 
    4407  
    4408 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
    4409 0.270 
    4410  
    4411 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
    4412 0.284 
    4413  
    4414 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
    4415 0.299 
    4416  
    4417 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
    4418 0.328 
    4419  
    4420 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
    4421 0.387 
    4422  
    4423 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405537 396.032 0.387 
    4424  
    4425 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405565 396.060 0.387 
    4426  
    4427 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406477 396.950 0.388 
    4428  
    4429 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407389 397.841 0.389 
    4430  
    4431 Read the alignment from file : alignment.ali 
    4432  
    4433 Total number of alignment positions: 229 
    4434  
    4435 # Code #_Res #_Segm PDB_code Name 
    4436 \------------------------------------------------------------------------------- 
    4437 1 chain_W_3 229 2 chain_W_3.2 
    4438 2 chain_W 229 2 chain_W 
    4439 check_a_343_> >> BEGINNING OF COMMAND 
    4440 openf___224_> Open ./chain_W_3.2.pdb 
    4441  
    4442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477814 466.615
    4443 0.456 
    4444  
    4445 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 477814 466.615 0.456 
    4446  
    4447 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477985 466.782
    4448 0.456 
    4449  
    4450 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478835 467.612
    4451 0.457 
    4452  
    4453 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480093 468.841
    4454 0.458 
    4455  
    4456 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481997 470.700
    4457 0.460 
    4458  
    4459 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481997 470.700 0.460 
    4460  
    4461 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482087 470.788
    4462 0.460 
    4463  
    4464 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 484943 473.577
    4465 0.462 
    4466  
    4467 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 484943 473.577 0.462 
    4468  
    4469 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485078 473.709
    4470 0.463 
    4471  
    4472 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489362 477.893
    4473 0.467 
    4474  
    4475 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489362 477.893 0.467 
    4476  
    4477 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489560 478.086
    4478 0.467 
    4479  
    4480 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495986 484.361
    4481 0.473 
    4482  
    4483 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495986 484.361 0.473 
    4484  
    4485 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496283 484.651
    4486 0.473 
    4487  
    4488 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505905 494.048
    4489 0.482 
    4490  
    4491 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505905 494.048 0.482 
    4492  
    4493 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506355 494.487
    4494 0.483 
    4495  
    4496 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    4497 0.497 
    4498  
    4499 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    4500  
    4501 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    4502 0.497 
    4503  
    4504 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    4505  
    4506 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521480 509.258
    4507 0.497 
    4508  
    4509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543138 530.408
    4510 0.518 
    4511  
    4512 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543138 530.408 0.518 
    4513  
    4514 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 544146 531.393
    4515 0.519 
    4516  
    4517 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543174 530.443
    4518 0.518 
    4519  
    4520 check_ali___> Checking the sequence-structure alignment. 
    4521  
    4522 Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: 
    4523  
    4524 ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST 
    4525 \---------------------------------------------- 
    4526 END OF TABLE 
    4527 check_a_344_>  Open ${LIB}/top_heav.lib 
    4528 read_to_681_> topology.submodel read from topology file: 3 
    4529 openf___224_> Open ${LIB}/par.lib 
    4530  
    4531 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682426 666.432
    4532 0.651 
    4533  
    4534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 684026 667.994
    4535 0.652 
    4536  
    4537 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688006 671.881
    4538 0.656 
    4539  
    4540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690006 673.834
    4541 0.658 
    4542  
    4543 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693006 676.764
    4544 0.661 
    4545  
    4546 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 697506 681.158
    4547 0.665 
    4548  
    4549 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703078 686.600
    4550 0.671 
    4551  
    4552 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705878 689.334
    4553 0.673 
    4554  
    4555 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710078 693.436
    4556 0.677 
    4557  
    4558 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 716378 699.588
    4559 0.683 
    4560  
    4561 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719150 702.295
    4562 0.686 
    4563  
    4564 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720550 703.662
    4565 0.687 
    4566 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 
    4567 227 561 661 112 0 
    4568  
    4569 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 738291 720.987 0.704 
    4570  
    4571 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 828353 808.938 0.790 
    4572  
    4573 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 841945 822.212 0.803 
    4574  
    4575 mkilst______> segment topology constructed from sequence and RTF: 
    4576 segments residues atoms bonds angles dihedrals impropers: 
    4577 1 114 900 921 0 0 389 
    4578  
    4579 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 880665 860.024 0.840 
    4580  
    4581 patch_______> segment topology patched using RTF: 1 ; SER ; NTER 
    4582 segments residues atoms bonds angles dihedrals impropers: 
    4583 1 114 900 921 1245 1488 389 
    4584  
    4585  
    4586 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 917761 896.251 0.875 
    4587 patch_______> segment topology patched using RTF: 114 ; LYS ; CTER 
    4588 segments residues atoms bonds angles dihedrals impropers: 
    4589 1 114 901 922 1247 1490 390 
    4590  
    4591 genseg______> segment topology constructed from sequence and RTF: 
    4592 segments residues atoms bonds angles dihedrals impropers: 
    4593 1 114 901 922 1247 1490 390 
    4594  
    4595 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 917789 896.278 0.875 
    4596  
    4597 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 935844 913.910 0.892 
    4598  
    4599 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1024632 1000.617 0.977 
    4600  
    4601 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1038320 1013.984 0.990 
    4602  
    4603 mkilst______> segment topology constructed from sequence and RTF: 
    4604 segments residues atoms bonds angles dihedrals impropers: 
    4605 2 229 1806 1848 1247 1490 781 
    4606  
    4607 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1077280 1052.031 1.027 
    4608  
    4609 patch_______> segment topology patched using RTF: 115 ; SER ; NTER 
    4610 segments residues atoms bonds angles dihedrals impropers: 
    4611 2 229 1806 1848 2499 2986 781 
    4612  
    4613  
    4614 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117016 1090.836 1.065 
    4615 patch_______> segment topology patched using RTF: 229 ; ALA ; CTER 
    4616 segments residues atoms bonds angles dihedrals impropers: 
    4617 2 229 1807 1849 2501 2988 782 
    4618  
    4619 genseg______> segment topology constructed from sequence and RTF: 
    4620 segments residues atoms bonds angles dihedrals impropers: 
    4621 2 229 1807 1849 2501 2988 782 
    4622  
    4623 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135520 1108.906 1.083 
    4624 patch_______> segment topology patched using RTF: 14 79 ; CYS CYS ; DISU 
    4625 segments residues atoms bonds angles dihedrals impropers: 
    4626 2 229 1807 1850 2503 2991 782 
    4627 patch_______> segment topology patched using RTF: 57 107 ; CYS CYS ; DISU 
    4628 segments residues atoms bonds angles dihedrals impropers: 
    4629 2 229 1807 1851 2505 2994 782 
    4630  
    4631 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135768 1109.148 1.083 
    4632 patch_______> segment topology patched using RTF: 67 109 ; CYS CYS ; DISU 
    4633 segments residues atoms bonds angles dihedrals impropers: 
    4634 2 229 1807 1852 2507 2997 782 
    4635 patch_______> segment topology patched using RTF: 128 193 ; CYS CYS ; DISU 
    4636 segments residues atoms bonds angles dihedrals impropers: 
    4637 2 229 1807 1853 2509 3000 782 
    4638 patch_______> segment topology patched using RTF: 171 221 ; CYS CYS ; DISU 
    4639 segments residues atoms bonds angles dihedrals impropers: 
    4640 2 229 1807 1854 2511 3003 782 
    4641 patch_______> segment topology patched using RTF: 181 223 ; CYS CYS ; DISU 
    4642 segments residues atoms bonds angles dihedrals impropers: 
    4643 2 229 1807 1855 2513 3006 782 
    4644 patch_s_522_> Number of disulfides patched in MODEL: 6 
    4645 transfe_506_> MODEL is an average of all templates. 
    4646 transfe_511_> Number of templates for coordinate transfer: 1 
    4647 After transferring coordinates of the equivalent template atoms, 
    4648 there are defined, undefined atoms in MODEL: 1807 0 
    4649 openf___224_> Open chain_W.ini 
    4650 wrpdb___568_> Residues, atoms, selected atoms: 229 1807 1807 
    4651 make_re_417_> Restraint type to be calculated: stereo 
    4652  
    4653 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1243217 1214.079
    4654 1.186 
    4655  
    4656 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251409 1222.079
    4657 1.193 
    4658  
    4659 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1267793 1238.079
    4660 1.209 
    4661  
    4662 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300561 1270.079
    4663 1.240 
    4664  
    4665 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1333329 1302.079
    4666 1.272 
    4667  
    4668 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398865 1366.079
    4669 1.334 
    4670  
    4671 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431633 1398.079
    4672 1.365 
    4673  
    4674 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1464401 1430.079
    4675 1.397 
    4676  
    4677 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529937 1494.079
    4678 1.459 
    4679  
    4680 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661009 1622.079
    4681 1.584 
    4682  
    4683 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1726545 1686.079
    4684 1.647 
    4685 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. 
    4686 Added bond,angle,dihedral,improper restraints : 1855 2513 2847 776 
    4687 Total number of restraints before, now : 0 7991 
    4688 make_re_422_> Number of previous, current restraints : 0 7991 
    4689 make_re_423_> Number of previous, current selected restraints: 0 7991 
    4690 make_re_417_> Restraint type to be calculated: phi-psi_binormal 
    4691  
    4692 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1857779 1814.237
    4693 1.772 
    4694 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin 
    4695 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt 
    4696 getdata_643_> Protein accepted: chain_W_3.2 
    4697 getdata_289_> Proteins (all/accepted): 1 1 
    4698  
    4699 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923331 1878.253
    4700 1.834 
    4701  
    4702 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054403 2006.253
    4703 1.959 
    4704 make_re_422_> Number of previous, current restraints : 7991 8216 
    4705 make_re_423_> Number of previous, current selected restraints: 7991 8216 
    4706 make_re_417_> Restraint type to be calculated: omega_dihedral 
    4707  
    4708 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4709 1.959 
    4710 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin 
    4711 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt 
    4712 getdata_643_> Protein accepted: chain_W_3.2 
    4713 getdata_289_> Proteins (all/accepted): 1 1 
    4714 omgdel__425_> Unselected all O C +N +CA dihedrals: 233 
    4715 (This is to avoid clashes between STEREO 
    4716 and OMEGA_DIHEDRAL restraints) 
    4717 make_re_422_> Number of previous, current restraints : 8216 8443 
    4718 make_re_423_> Number of previous, current selected restraints: 8216 8210 
    4719 make_re_417_> Restraint type to be calculated: chi1_dihedral 
    4720  
    4721 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4722 1.959 
    4723 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4724 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt 
    4725 getdata_643_> Protein accepted: chain_W_3.2 
    4726 getdata_289_> Proteins (all/accepted): 1 1 
    4727 make_re_422_> Number of previous, current restraints : 8443 8647 
    4728 make_re_423_> Number of previous, current selected restraints: 8210 8414 
    4729 make_re_417_> Restraint type to be calculated: chi2_dihedral 
    4730  
    4731 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    4732 1.959 
    4733 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4734 openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt 
    4735 getdata_643_> Protein accepted: chain_W_3.2 
    4736 getdata_289_> Proteins (all/accepted): 1 1 
    4737  
    4738 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185475 2134.253
    4739 2.084 
    4740 make_re_422_> Number of previous, current restraints : 8647 8775 
    4741 make_re_423_> Number of previous, current selected restraints: 8414 8542 
    4742 make_re_417_> Restraint type to be calculated: chi3_dihedral 
    4743  
    4744 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    4745 2.084 
    4746 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4747 openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt 
    4748 getdata_643_> Protein accepted: chain_W_3.2 
    4749 getdata_289_> Proteins (all/accepted): 1 1 
    4750 make_re_422_> Number of previous, current restraints : 8775 8827 
    4751 make_re_423_> Number of previous, current selected restraints: 8542 8594 
    4752 make_re_417_> Restraint type to be calculated: chi4_dihedral 
    4753  
    4754 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    4755 2.084 
    4756 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    4757 openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt 
    4758 mdtrsr__446W> A potential that relies on one protein is used, yet you have at 
    4759 least one known structure available. MDT, not library, potential is used. 
    4760 getdata_643_> Protein accepted: chain_W_3.2 
    4761 getdata_289_> Proteins (all/accepted): 1 1 
    4762 make_re_422_> Number of previous, current restraints : 8827 8857 
    4763 make_re_423_> Number of previous, current selected restraints: 8594 8624 
    4764 make_re_417_> Restraint type to be calculated: DISTANCE 
    4765  
    4766 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2705855 2642.437
    4767 2.581 
    4768  
    4769 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2967999 2898.437
    4770 2.831 
    4771  
    4772 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3099071 3026.437
    4773 2.956 
    4774 make_re_422_> Number of previous, current restraints : 8857 13008 
    4775 make_re_423_> Number of previous, current selected restraints: 8624 12775 
    4776 make_re_417_> Restraint type to be calculated: DISTANCE 
    4777  
    4778 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3361215 3282.437
    4779 3.206 
    4780 make_re_422_> Number of previous, current restraints : 13008 17456 
    4781 make_re_423_> Number of previous, current selected restraints: 12775 17223 
    4782 make_re_417_> Restraint type to be calculated: DISTANCE 
    4783  
    4784 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3885503 3794.437
    4785 3.706 
    4786 make_re_422_> Number of previous, current restraints : 17456 21500 
    4787 make_re_423_> Number of previous, current selected restraints: 17223 21267 
    4788 make_re_417_> Restraint type to be calculated: DISTANCE 
    4789  
    4790 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4147647 4050.437
    4791 3.956 
    4792 make_re_422_> Number of previous, current restraints : 21500 23481 
    4793 make_re_423_> Number of previous, current selected restraints: 21267 23248 
    4794 0 atoms in HETATM/BLK residues constrained 
    4795 to protein atoms within 2.30 angstroms 
    4796 and protein CA atoms within 10.00 angstroms 
    4797 make_re_417_> Restraint type to be calculated: DISTANCE 
    4798 make_re_422_> Number of previous, current restraints : 23481 23481 
    4799 make_re_423_> Number of previous, current selected restraints: 23248 23248 
    4800 make_re_417_> Restraint type to be calculated: DISTANCE 
    4801 make_re_422_> Number of previous, current restraints : 23481 23481 
    4802 make_re_423_> Number of previous, current selected restraints: 23248 23248 
    4803 make_re_417_> Restraint type to be calculated: DISTANCE 
    4804 make_re_422_> Number of previous, current restraints : 23481 23481 
    4805 make_re_423_> Number of previous, current selected restraints: 23248 23248 
    4806 make_re_417_> Restraint type to be calculated: DISTANCE 
    4807 make_re_422_> Number of previous, current restraints : 23481 23481 
    4808 make_re_423_> Number of previous, current selected restraints: 23248 23248 
    4809 0 atoms in residues without defined topology 
    4810 constrained to be rigid bodies 
    4811 make_re_417_> Restraint type to be calculated: DISTANCE 
    4812 make_re_422_> Number of previous, current restraints : 23481 23481 
    4813 make_re_423_> Number of previous, current selected restraints: 23248 23248 
    4814 rmdupl__427_> 1360 redundant cosine dihedral restraints were unselected. 
    4815 condens_443_> Restraints marked for deletion were removed. 
    4816 Total number of restraints before, now: 23481 21888 
    4817 openf___224_> Open chain_W.rsr 
    4818 openf___224_> Open chain_W.rsr 
    4819  
    4820 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4260279 4160.429
    4821 4.063 
    4822 rdcsr2__307_> Number of restraints read : 21888 
    4823 Number of excluded pairs read: 0 
    4824 Number of pseudo atoms read : 0 
    4825 rdcsrs__304_> Restraints in memory, selected restraints: 21888 21888 
    4826 Explicitly excluded atom pairs in memory : 0 
    4827 Pseudo atoms in memory : 0 
    4828  
    4829 No output models from Modeller; see log for Modeller text output. 
    4830 Modeller job (ID 4N4DRLUWRS52AZE2) finished 
    4831  
    4832 Modeller error output 
    4833 Traceback (most recent call last): 
    4834 File "ModellerModelling.py", line 93, in   
    4835 a.make() 
    4836 File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
    4837 line 42, in make 
    4838 AutoModel.make(self, exit_stage) 
    4839 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    4840 line 151, in make 
    4841 atmsel = self._check_select_atoms() 
    4842 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    4843 line 700, in _check_select_atoms 
    4844 raise ModellerError("no atoms selected for optimization") 
    4845 _modeller.ModellerError: no atoms selected for optimization 
    4846  
    4847  
    4848 Modeller run output 
    4849  
    4850 MODELLER 10.6, 2024/10/17, r12888 
    4851  
    4852 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    4853  
    4854  
    4855 Copyright(c) 1989-2024 Andrej Sali 
    4856 All Rights Reserved 
    4857  
    4858 Written by A. Sali 
    4859 with help from 
    4860 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    4861 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    4862 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    4863 F. Melo, J.P. Overington, E. Feyfant 
    4864 University of California, San Francisco, USA 
    4865 Rockefeller University, New York, USA 
    4866 Harvard University, Cambridge, USA 
    4867 Imperial Cancer Research Fund, London, UK 
    4868 Birkbeck College, University of London, London, UK 
    4869  
    4870  
    4871 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    4872 4.18.0-553.44.1.el8_10.x86_64 x86_64 
    4873 Date and time of compilation : 2024/10/17 20:43:03 
    4874 MODELLER executable type : x86_64-intel8 
    4875 Job starting time (YY/MM/DD HH:MM:SS): 2025/04/03 10:33:44 
    4876  
    4877 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    4878 openf___224_> Open $(LIB)/restyp.lib 
    4879 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    4880 rdresgr_266_> Number of residue groups: 2 
    4881 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    4882  
    4883 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    4884 0.183 
    4885  
    4886 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    4887 0.183 
    4888 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    4889  
    4890 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    4891 0.230 
    4892 rdrdih__263_> Number of dihedral angle types : 9 
    4893 Maximal number of dihedral angle optima: 3 
    4894 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    4895 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    4896  
    4897 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    4898 0.242 
    4899 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    4900 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    4901 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    4902 rdclass_257_> Number of classes: 5 
    4903 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    4904 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    4905 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    4906 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    4907 rdrrwgh_268_> Number of residue types: 21 
    4908 dope_loopm_W> The class 'dope_loopmodel' is deprecated; use 'DOPELoopModel'
    4909 instead 
    4910 openf___224_> Open alignment.ali 
    4911  
    4912 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
    4913 0.270 
    4914  
    4915 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
    4916 0.284 
    4917  
    4918 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
    4919 0.299 
    4920  
    4921 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
    4922 0.328 
    4923  
    4924 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
    4925 0.387 
    4926  
    4927 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405537 396.032 0.387 
    4928  
    4929 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405565 396.060 0.387 
    4930  
    4931 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406477 396.950 0.388 
    4932  
    4933 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407389 397.841 0.389 
    4934  
    4935 Read the alignment from file : alignment.ali 
    4936  
    4937 Total number of alignment positions: 229 
    4938  
    4939 # Code #_Res #_Segm PDB_code Name 
    4940 \------------------------------------------------------------------------------- 
    4941 1 chain_W_3 229 2 chain_W_3.1 
    4942 2 chain_W 229 2 chain_W 
    4943 check_a_343_> >> BEGINNING OF COMMAND 
    4944 openf___224_> Open ./chain_W_3.1.pdb 
    4945  
    4946 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477814 466.615
    4947 0.456 
    4948  
    4949 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 477814 466.615 0.456 
    4950  
    4951 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477985 466.782
    4952 0.456 
    4953  
    4954 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478835 467.612
    4955 0.457 
    4956  
    4957 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480093 468.841
    4958 0.458 
    4959  
    4960 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481997 470.700
    4961 0.460 
    4962  
    4963 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481997 470.700 0.460 
    4964  
    4965 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482087 470.788
    4966 0.460 
    4967  
    4968 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 484943 473.577
    4969 0.462 
    4970  
    4971 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 484943 473.577 0.462 
    4972  
    4973 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485078 473.709
    4974 0.463 
    4975  
    4976 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489362 477.893
    4977 0.467 
    4978  
    4979 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489362 477.893 0.467 
    4980  
    4981 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489560 478.086
    4982 0.467 
    4983  
    4984 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495986 484.361
    4985 0.473 
    4986  
    4987 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495986 484.361 0.473 
    4988  
    4989 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496283 484.651
    4990 0.473 
    4991  
    4992 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505905 494.048
    4993 0.482 
    4994  
    4995 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505905 494.048 0.482 
    4996  
    4997 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506355 494.487
    4998 0.483 
    4999  
    5000 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    5001 0.497 
    5002  
    5003 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    5004  
    5005 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    5006 0.497 
    5007  
    5008 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    5009  
    5010 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521480 509.258
    5011 0.497 
    5012  
    5013 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543138 530.408
    5014 0.518 
    5015  
    5016 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543138 530.408 0.518 
    5017  
    5018 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 544146 531.393
    5019 0.519 
    5020  
    5021 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543174 530.443
    5022 0.518 
    5023  
    5024 check_ali___> Checking the sequence-structure alignment. 
    5025  
    5026 Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: 
    5027  
    5028 ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST 
    5029 \---------------------------------------------- 
    5030 END OF TABLE 
    5031 check_a_344_>  Open ${LIB}/top_heav.lib 
    5032 read_to_681_> topology.submodel read from topology file: 3 
    5033 openf___224_> Open ${LIB}/par.lib 
    5034  
    5035 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682426 666.432
    5036 0.651 
    5037  
    5038 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 684026 667.994
    5039 0.652 
    5040  
    5041 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688006 671.881
    5042 0.656 
    5043  
    5044 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690006 673.834
    5045 0.658 
    5046  
    5047 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693006 676.764
    5048 0.661 
    5049  
    5050 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 697506 681.158
    5051 0.665 
    5052  
    5053 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703078 686.600
    5054 0.671 
    5055  
    5056 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705878 689.334
    5057 0.673 
    5058  
    5059 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710078 693.436
    5060 0.677 
    5061  
    5062 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 716378 699.588
    5063 0.683 
    5064  
    5065 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719150 702.295
    5066 0.686 
    5067  
    5068 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720550 703.662
    5069 0.687 
    5070 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 
    5071 227 561 661 112 0 
    5072  
    5073 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 738291 720.987 0.704 
    5074  
    5075 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 828353 808.938 0.790 
    5076  
    5077 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 841945 822.212 0.803 
    5078  
    5079 mkilst______> segment topology constructed from sequence and RTF: 
    5080 segments residues atoms bonds angles dihedrals impropers: 
    5081 1 114 900 921 0 0 389 
    5082  
    5083 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 880665 860.024 0.840 
    5084  
    5085 patch_______> segment topology patched using RTF: 1 ; SER ; NTER 
    5086 segments residues atoms bonds angles dihedrals impropers: 
    5087 1 114 900 921 1245 1488 389 
    5088  
    5089  
    5090 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 917761 896.251 0.875 
    5091 patch_______> segment topology patched using RTF: 114 ; LYS ; CTER 
    5092 segments residues atoms bonds angles dihedrals impropers: 
    5093 1 114 901 922 1247 1490 390 
    5094  
    5095 genseg______> segment topology constructed from sequence and RTF: 
    5096 segments residues atoms bonds angles dihedrals impropers: 
    5097 1 114 901 922 1247 1490 390 
    5098  
    5099 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 917789 896.278 0.875 
    5100  
    5101 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 935844 913.910 0.892 
    5102  
    5103 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1024632 1000.617 0.977 
    5104  
    5105 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1038320 1013.984 0.990 
    5106  
    5107 mkilst______> segment topology constructed from sequence and RTF: 
    5108 segments residues atoms bonds angles dihedrals impropers: 
    5109 2 229 1806 1848 1247 1490 781 
    5110  
    5111 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1077280 1052.031 1.027 
    5112  
    5113 patch_______> segment topology patched using RTF: 115 ; SER ; NTER 
    5114 segments residues atoms bonds angles dihedrals impropers: 
    5115 2 229 1806 1848 2499 2986 781 
    5116  
    5117  
    5118 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117016 1090.836 1.065 
    5119 patch_______> segment topology patched using RTF: 229 ; ALA ; CTER 
    5120 segments residues atoms bonds angles dihedrals impropers: 
    5121 2 229 1807 1849 2501 2988 782 
    5122  
    5123 genseg______> segment topology constructed from sequence and RTF: 
    5124 segments residues atoms bonds angles dihedrals impropers: 
    5125 2 229 1807 1849 2501 2988 782 
    5126  
    5127 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135520 1108.906 1.083 
    5128 patch_______> segment topology patched using RTF: 14 79 ; CYS CYS ; DISU 
    5129 segments residues atoms bonds angles dihedrals impropers: 
    5130 2 229 1807 1850 2503 2991 782 
    5131 patch_______> segment topology patched using RTF: 57 107 ; CYS CYS ; DISU 
    5132 segments residues atoms bonds angles dihedrals impropers: 
    5133 2 229 1807 1851 2505 2994 782 
    5134  
    5135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135768 1109.148 1.083 
    5136 patch_______> segment topology patched using RTF: 67 109 ; CYS CYS ; DISU 
    5137 segments residues atoms bonds angles dihedrals impropers: 
    5138 2 229 1807 1852 2507 2997 782 
    5139 patch_______> segment topology patched using RTF: 128 193 ; CYS CYS ; DISU 
    5140 segments residues atoms bonds angles dihedrals impropers: 
    5141 2 229 1807 1853 2509 3000 782 
    5142 patch_______> segment topology patched using RTF: 171 221 ; CYS CYS ; DISU 
    5143 segments residues atoms bonds angles dihedrals impropers: 
    5144 2 229 1807 1854 2511 3003 782 
    5145 patch_______> segment topology patched using RTF: 181 223 ; CYS CYS ; DISU 
    5146 segments residues atoms bonds angles dihedrals impropers: 
    5147 2 229 1807 1855 2513 3006 782 
    5148 patch_s_522_> Number of disulfides patched in MODEL: 6 
    5149 transfe_506_> MODEL is an average of all templates. 
    5150 transfe_511_> Number of templates for coordinate transfer: 1 
    5151 After transferring coordinates of the equivalent template atoms, 
    5152 there are defined, undefined atoms in MODEL: 1807 0 
    5153 openf___224_> Open chain_W.ini 
    5154 wrpdb___568_> Residues, atoms, selected atoms: 229 1807 1807 
    5155 make_re_417_> Restraint type to be calculated: stereo 
    5156  
    5157 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1243217 1214.079
    5158 1.186 
    5159  
    5160 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251409 1222.079
    5161 1.193 
    5162  
    5163 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1267793 1238.079
    5164 1.209 
    5165  
    5166 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300561 1270.079
    5167 1.240 
    5168  
    5169 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1333329 1302.079
    5170 1.272 
    5171  
    5172 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398865 1366.079
    5173 1.334 
    5174  
    5175 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431633 1398.079
    5176 1.365 
    5177  
    5178 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1464401 1430.079
    5179 1.397 
    5180  
    5181 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529937 1494.079
    5182 1.459 
    5183  
    5184 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661009 1622.079
    5185 1.584 
    5186  
    5187 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1726545 1686.079
    5188 1.647 
    5189 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. 
    5190 Added bond,angle,dihedral,improper restraints : 1855 2513 2847 776 
    5191 Total number of restraints before, now : 0 7991 
    5192 make_re_422_> Number of previous, current restraints : 0 7991 
    5193 make_re_423_> Number of previous, current selected restraints: 0 7991 
    5194 make_re_417_> Restraint type to be calculated: phi-psi_binormal 
    5195  
    5196 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1857779 1814.237
    5197 1.772 
    5198 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin 
    5199 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt 
    5200 getdata_643_> Protein accepted: chain_W_3.1 
    5201 getdata_289_> Proteins (all/accepted): 1 1 
    5202  
    5203 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923331 1878.253
    5204 1.834 
    5205  
    5206 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054403 2006.253
    5207 1.959 
    5208 make_re_422_> Number of previous, current restraints : 7991 8216 
    5209 make_re_423_> Number of previous, current selected restraints: 7991 8216 
    5210 make_re_417_> Restraint type to be calculated: omega_dihedral 
    5211  
    5212 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5213 1.959 
    5214 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin 
    5215 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt 
    5216 getdata_643_> Protein accepted: chain_W_3.1 
    5217 getdata_289_> Proteins (all/accepted): 1 1 
    5218 omgdel__425_> Unselected all O C +N +CA dihedrals: 233 
    5219 (This is to avoid clashes between STEREO 
    5220 and OMEGA_DIHEDRAL restraints) 
    5221 make_re_422_> Number of previous, current restraints : 8216 8443 
    5222 make_re_423_> Number of previous, current selected restraints: 8216 8210 
    5223 make_re_417_> Restraint type to be calculated: chi1_dihedral 
    5224  
    5225 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5226 1.959 
    5227 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5228 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt 
    5229 getdata_643_> Protein accepted: chain_W_3.1 
    5230 getdata_289_> Proteins (all/accepted): 1 1 
    5231 make_re_422_> Number of previous, current restraints : 8443 8647 
    5232 make_re_423_> Number of previous, current selected restraints: 8210 8414 
    5233 make_re_417_> Restraint type to be calculated: chi2_dihedral 
    5234  
    5235 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5236 1.959 
    5237 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5238 openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt 
    5239 getdata_643_> Protein accepted: chain_W_3.1 
    5240 getdata_289_> Proteins (all/accepted): 1 1 
    5241  
    5242 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185475 2134.253
    5243 2.084 
    5244 make_re_422_> Number of previous, current restraints : 8647 8775 
    5245 make_re_423_> Number of previous, current selected restraints: 8414 8542 
    5246 make_re_417_> Restraint type to be calculated: chi3_dihedral 
    5247  
    5248 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    5249 2.084 
    5250 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5251 openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt 
    5252 getdata_643_> Protein accepted: chain_W_3.1 
    5253 getdata_289_> Proteins (all/accepted): 1 1 
    5254 make_re_422_> Number of previous, current restraints : 8775 8827 
    5255 make_re_423_> Number of previous, current selected restraints: 8542 8594 
    5256 make_re_417_> Restraint type to be calculated: chi4_dihedral 
    5257  
    5258 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    5259 2.084 
    5260 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5261 openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt 
    5262 mdtrsr__446W> A potential that relies on one protein is used, yet you have at 
    5263 least one known structure available. MDT, not library, potential is used. 
    5264 getdata_643_> Protein accepted: chain_W_3.1 
    5265 getdata_289_> Proteins (all/accepted): 1 1 
    5266 make_re_422_> Number of previous, current restraints : 8827 8857 
    5267 make_re_423_> Number of previous, current selected restraints: 8594 8624 
    5268 make_re_417_> Restraint type to be calculated: DISTANCE 
    5269  
    5270 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2705855 2642.437
    5271 2.581 
    5272  
    5273 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2967999 2898.437
    5274 2.831 
    5275  
    5276 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3099071 3026.437
    5277 2.956 
    5278 make_re_422_> Number of previous, current restraints : 8857 13023 
    5279 make_re_423_> Number of previous, current selected restraints: 8624 12790 
    5280 make_re_417_> Restraint type to be calculated: DISTANCE 
    5281  
    5282 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3361215 3282.437
    5283 3.206 
    5284 make_re_422_> Number of previous, current restraints : 13023 17475 
    5285 make_re_423_> Number of previous, current selected restraints: 12790 17242 
    5286 make_re_417_> Restraint type to be calculated: DISTANCE 
    5287  
    5288 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3885503 3794.437
    5289 3.706 
    5290 make_re_422_> Number of previous, current restraints : 17475 21539 
    5291 make_re_423_> Number of previous, current selected restraints: 17242 21306 
    5292 make_re_417_> Restraint type to be calculated: DISTANCE 
    5293  
    5294 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4147647 4050.437
    5295 3.956 
    5296 make_re_422_> Number of previous, current restraints : 21539 23531 
    5297 make_re_423_> Number of previous, current selected restraints: 21306 23298 
    5298 0 atoms in HETATM/BLK residues constrained 
    5299 to protein atoms within 2.30 angstroms 
    5300 and protein CA atoms within 10.00 angstroms 
    5301 make_re_417_> Restraint type to be calculated: DISTANCE 
    5302 make_re_422_> Number of previous, current restraints : 23531 23531 
    5303 make_re_423_> Number of previous, current selected restraints: 23298 23298 
    5304 make_re_417_> Restraint type to be calculated: DISTANCE 
    5305 make_re_422_> Number of previous, current restraints : 23531 23531 
    5306 make_re_423_> Number of previous, current selected restraints: 23298 23298 
    5307 make_re_417_> Restraint type to be calculated: DISTANCE 
    5308 make_re_422_> Number of previous, current restraints : 23531 23531 
    5309 make_re_423_> Number of previous, current selected restraints: 23298 23298 
    5310 make_re_417_> Restraint type to be calculated: DISTANCE 
    5311 make_re_422_> Number of previous, current restraints : 23531 23531 
    5312 make_re_423_> Number of previous, current selected restraints: 23298 23298 
    5313 0 atoms in residues without defined topology 
    5314 constrained to be rigid bodies 
    5315 make_re_417_> Restraint type to be calculated: DISTANCE 
    5316 make_re_422_> Number of previous, current restraints : 23531 23531 
    5317 make_re_423_> Number of previous, current selected restraints: 23298 23298 
    5318 rmdupl__427_> 1360 redundant cosine dihedral restraints were unselected. 
    5319 condens_443_> Restraints marked for deletion were removed. 
    5320 Total number of restraints before, now: 23531 21938 
    5321 openf___224_> Open chain_W.rsr 
    5322 openf___224_> Open chain_W.rsr 
    5323  
    5324 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4260279 4160.429
    5325 4.063 
    5326 rdcsr2__307_> Number of restraints read : 21938 
    5327 Number of excluded pairs read: 0 
    5328 Number of pseudo atoms read : 0 
    5329 rdcsrs__304_> Restraints in memory, selected restraints: 21938 21938 
    5330 Explicitly excluded atom pairs in memory : 0 
    5331 Pseudo atoms in memory : 0 
    5332  
    5333 No output models from Modeller; see log for Modeller text output. 
    5334 Modeller job (ID 9768OIBIUKACZK45) finished 
    5335  
    5336 Modeller error output 
    5337 Traceback (most recent call last): 
    5338 File "ModellerModelling.py", line 93, in   
    5339 a.make() 
    5340 File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
    5341 line 42, in make 
    5342 AutoModel.make(self, exit_stage) 
    5343 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    5344 line 151, in make 
    5345 atmsel = self._check_select_atoms() 
    5346 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    5347 line 700, in _check_select_atoms 
    5348 raise ModellerError("no atoms selected for optimization") 
    5349 _modeller.ModellerError: no atoms selected for optimization 
    5350  
    5351  
    5352 Modeller run output 
    5353  
    5354 MODELLER 10.6, 2024/10/17, r12888 
    5355  
    5356 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    5357  
    5358  
    5359 Copyright(c) 1989-2024 Andrej Sali 
    5360 All Rights Reserved 
    5361  
    5362 Written by A. Sali 
    5363 with help from 
    5364 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    5365 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    5366 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    5367 F. Melo, J.P. Overington, E. Feyfant 
    5368 University of California, San Francisco, USA 
    5369 Rockefeller University, New York, USA 
    5370 Harvard University, Cambridge, USA 
    5371 Imperial Cancer Research Fund, London, UK 
    5372 Birkbeck College, University of London, London, UK 
    5373  
    5374  
    5375 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    5376 4.18.0-553.44.1.el8_10.x86_64 x86_64 
    5377 Date and time of compilation : 2024/10/17 20:43:03 
    5378 MODELLER executable type : x86_64-intel8 
    5379 Job starting time (YY/MM/DD HH:MM:SS): 2025/04/03 10:33:45 
    5380  
    5381 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    5382 openf___224_> Open $(LIB)/restyp.lib 
    5383 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    5384 rdresgr_266_> Number of residue groups: 2 
    5385 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    5386  
    5387 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    5388 0.183 
    5389  
    5390 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    5391 0.183 
    5392 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    5393  
    5394 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    5395 0.230 
    5396 rdrdih__263_> Number of dihedral angle types : 9 
    5397 Maximal number of dihedral angle optima: 3 
    5398 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    5399 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    5400  
    5401 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    5402 0.242 
    5403 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    5404 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    5405 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    5406 rdclass_257_> Number of classes: 5 
    5407 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    5408 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    5409 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    5410 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    5411 rdrrwgh_268_> Number of residue types: 21 
    5412 dope_loopm_W> The class 'dope_loopmodel' is deprecated; use 'DOPELoopModel'
    5413 instead 
    5414 openf___224_> Open alignment.ali 
    5415  
    5416 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
    5417 0.270 
    5418  
    5419 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
    5420 0.284 
    5421  
    5422 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
    5423 0.299 
    5424  
    5425 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
    5426 0.328 
    5427  
    5428 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
    5429 0.387 
    5430  
    5431 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405537 396.032 0.387 
    5432  
    5433 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405565 396.060 0.387 
    5434  
    5435 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406477 396.950 0.388 
    5436  
    5437 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407389 397.841 0.389 
    5438  
    5439 Read the alignment from file : alignment.ali 
    5440  
    5441 Total number of alignment positions: 229 
    5442  
    5443 # Code #_Res #_Segm PDB_code Name 
    5444 \------------------------------------------------------------------------------- 
    5445 1 chain_W_3 229 2 chain_W_3.4 
    5446 2 chain_W 229 2 chain_W 
    5447 check_a_343_> >> BEGINNING OF COMMAND 
    5448 openf___224_> Open ./chain_W_3.4.pdb 
    5449  
    5450 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477814 466.615
    5451 0.456 
    5452  
    5453 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 477814 466.615 0.456 
    5454  
    5455 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477985 466.782
    5456 0.456 
    5457  
    5458 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478835 467.612
    5459 0.457 
    5460  
    5461 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480093 468.841
    5462 0.458 
    5463  
    5464 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481997 470.700
    5465 0.460 
    5466  
    5467 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481997 470.700 0.460 
    5468  
    5469 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482087 470.788
    5470 0.460 
    5471  
    5472 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 484943 473.577
    5473 0.462 
    5474  
    5475 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 484943 473.577 0.462 
    5476  
    5477 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485078 473.709
    5478 0.463 
    5479  
    5480 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489362 477.893
    5481 0.467 
    5482  
    5483 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489362 477.893 0.467 
    5484  
    5485 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489560 478.086
    5486 0.467 
    5487  
    5488 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495986 484.361
    5489 0.473 
    5490  
    5491 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495986 484.361 0.473 
    5492  
    5493 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496283 484.651
    5494 0.473 
    5495  
    5496 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505905 494.048
    5497 0.482 
    5498  
    5499 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505905 494.048 0.482 
    5500  
    5501 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506355 494.487
    5502 0.483 
    5503  
    5504 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    5505 0.497 
    5506  
    5507 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    5508  
    5509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
    5510 0.497 
    5511  
    5512 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497 
    5513  
    5514 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521480 509.258
    5515 0.497 
    5516  
    5517 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543138 530.408
    5518 0.518 
    5519  
    5520 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543138 530.408 0.518 
    5521  
    5522 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 544146 531.393
    5523 0.519 
    5524  
    5525 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543174 530.443
    5526 0.518 
    5527  
    5528 check_ali___> Checking the sequence-structure alignment. 
    5529  
    5530 Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: 
    5531  
    5532 ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST 
    5533 \---------------------------------------------- 
    5534 END OF TABLE 
    5535 check_a_344_>  Open ${LIB}/top_heav.lib 
    5536 read_to_681_> topology.submodel read from topology file: 3 
    5537 openf___224_> Open ${LIB}/par.lib 
    5538  
    5539 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682426 666.432
    5540 0.651 
    5541  
    5542 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 684026 667.994
    5543 0.652 
    5544  
    5545 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688006 671.881
    5546 0.656 
    5547  
    5548 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690006 673.834
    5549 0.658 
    5550  
    5551 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693006 676.764
    5552 0.661 
    5553  
    5554 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 697506 681.158
    5555 0.665 
    5556  
    5557 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703078 686.600
    5558 0.671 
    5559  
    5560 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705878 689.334
    5561 0.673 
    5562  
    5563 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710078 693.436
    5564 0.677 
    5565  
    5566 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 716378 699.588
    5567 0.683 
    5568  
    5569 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719150 702.295
    5570 0.686 
    5571  
    5572 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720550 703.662
    5573 0.687 
    5574 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 
    5575 227 561 661 112 0 
    5576  
    5577 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 738291 720.987 0.704 
    5578  
    5579 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 828353 808.938 0.790 
    5580  
    5581 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 841945 822.212 0.803 
    5582  
    5583 mkilst______> segment topology constructed from sequence and RTF: 
    5584 segments residues atoms bonds angles dihedrals impropers: 
    5585 1 114 900 921 0 0 389 
    5586  
    5587 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 880665 860.024 0.840 
    5588  
    5589 patch_______> segment topology patched using RTF: 1 ; SER ; NTER 
    5590 segments residues atoms bonds angles dihedrals impropers: 
    5591 1 114 900 921 1245 1488 389 
    5592  
    5593  
    5594 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 917761 896.251 0.875 
    5595 patch_______> segment topology patched using RTF: 114 ; LYS ; CTER 
    5596 segments residues atoms bonds angles dihedrals impropers: 
    5597 1 114 901 922 1247 1490 390 
    5598  
    5599 genseg______> segment topology constructed from sequence and RTF: 
    5600 segments residues atoms bonds angles dihedrals impropers: 
    5601 1 114 901 922 1247 1490 390 
    5602  
    5603 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 917789 896.278 0.875 
    5604  
    5605 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 935844 913.910 0.892 
    5606  
    5607 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1024632 1000.617 0.977 
    5608  
    5609 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1038320 1013.984 0.990 
    5610  
    5611 mkilst______> segment topology constructed from sequence and RTF: 
    5612 segments residues atoms bonds angles dihedrals impropers: 
    5613 2 229 1806 1848 1247 1490 781 
    5614  
    5615 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1077280 1052.031 1.027 
    5616  
    5617 patch_______> segment topology patched using RTF: 115 ; SER ; NTER 
    5618 segments residues atoms bonds angles dihedrals impropers: 
    5619 2 229 1806 1848 2499 2986 781 
    5620  
    5621  
    5622 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117016 1090.836 1.065 
    5623 patch_______> segment topology patched using RTF: 229 ; ALA ; CTER 
    5624 segments residues atoms bonds angles dihedrals impropers: 
    5625 2 229 1807 1849 2501 2988 782 
    5626  
    5627 genseg______> segment topology constructed from sequence and RTF: 
    5628 segments residues atoms bonds angles dihedrals impropers: 
    5629 2 229 1807 1849 2501 2988 782 
    5630  
    5631 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135520 1108.906 1.083 
    5632 patch_______> segment topology patched using RTF: 14 79 ; CYS CYS ; DISU 
    5633 segments residues atoms bonds angles dihedrals impropers: 
    5634 2 229 1807 1850 2503 2991 782 
    5635 patch_______> segment topology patched using RTF: 57 107 ; CYS CYS ; DISU 
    5636 segments residues atoms bonds angles dihedrals impropers: 
    5637 2 229 1807 1851 2505 2994 782 
    5638  
    5639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135768 1109.148 1.083 
    5640 patch_______> segment topology patched using RTF: 67 109 ; CYS CYS ; DISU 
    5641 segments residues atoms bonds angles dihedrals impropers: 
    5642 2 229 1807 1852 2507 2997 782 
    5643 patch_______> segment topology patched using RTF: 128 193 ; CYS CYS ; DISU 
    5644 segments residues atoms bonds angles dihedrals impropers: 
    5645 2 229 1807 1853 2509 3000 782 
    5646 patch_______> segment topology patched using RTF: 171 221 ; CYS CYS ; DISU 
    5647 segments residues atoms bonds angles dihedrals impropers: 
    5648 2 229 1807 1854 2511 3003 782 
    5649 patch_______> segment topology patched using RTF: 181 223 ; CYS CYS ; DISU 
    5650 segments residues atoms bonds angles dihedrals impropers: 
    5651 2 229 1807 1855 2513 3006 782 
    5652 patch_s_522_> Number of disulfides patched in MODEL: 6 
    5653 transfe_506_> MODEL is an average of all templates. 
    5654 transfe_511_> Number of templates for coordinate transfer: 1 
    5655 After transferring coordinates of the equivalent template atoms, 
    5656 there are defined, undefined atoms in MODEL: 1807 0 
    5657 openf___224_> Open chain_W.ini 
    5658 wrpdb___568_> Residues, atoms, selected atoms: 229 1807 1807 
    5659 make_re_417_> Restraint type to be calculated: stereo 
    5660  
    5661 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1243217 1214.079
    5662 1.186 
    5663  
    5664 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251409 1222.079
    5665 1.193 
    5666  
    5667 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1267793 1238.079
    5668 1.209 
    5669  
    5670 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300561 1270.079
    5671 1.240 
    5672  
    5673 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1333329 1302.079
    5674 1.272 
    5675  
    5676 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398865 1366.079
    5677 1.334 
    5678  
    5679 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431633 1398.079
    5680 1.365 
    5681  
    5682 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1464401 1430.079
    5683 1.397 
    5684  
    5685 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529937 1494.079
    5686 1.459 
    5687  
    5688 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661009 1622.079
    5689 1.584 
    5690  
    5691 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1726545 1686.079
    5692 1.647 
    5693 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. 
    5694 Added bond,angle,dihedral,improper restraints : 1855 2513 2847 776 
    5695 Total number of restraints before, now : 0 7991 
    5696 make_re_422_> Number of previous, current restraints : 0 7991 
    5697 make_re_423_> Number of previous, current selected restraints: 0 7991 
    5698 make_re_417_> Restraint type to be calculated: phi-psi_binormal 
    5699  
    5700 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1857779 1814.237
    5701 1.772 
    5702 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin 
    5703 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt 
    5704 getdata_643_> Protein accepted: chain_W_3.4 
    5705 getdata_289_> Proteins (all/accepted): 1 1 
    5706  
    5707 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923331 1878.253
    5708 1.834 
    5709  
    5710 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054403 2006.253
    5711 1.959 
    5712 make_re_422_> Number of previous, current restraints : 7991 8216 
    5713 make_re_423_> Number of previous, current selected restraints: 7991 8216 
    5714 make_re_417_> Restraint type to be calculated: omega_dihedral 
    5715  
    5716 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5717 1.959 
    5718 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin 
    5719 openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt 
    5720 getdata_643_> Protein accepted: chain_W_3.4 
    5721 getdata_289_> Proteins (all/accepted): 1 1 
    5722 omgdel__425_> Unselected all O C +N +CA dihedrals: 233 
    5723 (This is to avoid clashes between STEREO 
    5724 and OMEGA_DIHEDRAL restraints) 
    5725 make_re_422_> Number of previous, current restraints : 8216 8443 
    5726 make_re_423_> Number of previous, current selected restraints: 8216 8210 
    5727 make_re_417_> Restraint type to be calculated: chi1_dihedral 
    5728  
    5729 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5730 1.959 
    5731 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5732 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt 
    5733 getdata_643_> Protein accepted: chain_W_3.4 
    5734 getdata_289_> Proteins (all/accepted): 1 1 
    5735 make_re_422_> Number of previous, current restraints : 8443 8647 
    5736 make_re_423_> Number of previous, current selected restraints: 8210 8414 
    5737 make_re_417_> Restraint type to be calculated: chi2_dihedral 
    5738  
    5739 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
    5740 1.959 
    5741 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5742 openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt 
    5743 getdata_643_> Protein accepted: chain_W_3.4 
    5744 getdata_289_> Proteins (all/accepted): 1 1 
    5745  
    5746 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185475 2134.253
    5747 2.084 
    5748 make_re_422_> Number of previous, current restraints : 8647 8775 
    5749 make_re_423_> Number of previous, current selected restraints: 8414 8542 
    5750 make_re_417_> Restraint type to be calculated: chi3_dihedral 
    5751  
    5752 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    5753 2.084 
    5754 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5755 openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt 
    5756 getdata_643_> Protein accepted: chain_W_3.4 
    5757 getdata_289_> Proteins (all/accepted): 1 1 
    5758 make_re_422_> Number of previous, current restraints : 8775 8827 
    5759 make_re_423_> Number of previous, current selected restraints: 8542 8594 
    5760 make_re_417_> Restraint type to be calculated: chi4_dihedral 
    5761  
    5762 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
    5763 2.084 
    5764 openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin 
    5765 openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt 
    5766 mdtrsr__446W> A potential that relies on one protein is used, yet you have at 
    5767 least one known structure available. MDT, not library, potential is used. 
    5768 getdata_643_> Protein accepted: chain_W_3.4 
    5769 getdata_289_> Proteins (all/accepted): 1 1 
    5770 make_re_422_> Number of previous, current restraints : 8827 8857 
    5771 make_re_423_> Number of previous, current selected restraints: 8594 8624 
    5772 make_re_417_> Restraint type to be calculated: DISTANCE 
    5773  
    5774 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2705855 2642.437
    5775 2.581 
    5776  
    5777 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2967999 2898.437
    5778 2.831 
    5779  
    5780 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3099071 3026.437
    5781 2.956 
    5782 make_re_422_> Number of previous, current restraints : 8857 13005 
    5783 make_re_423_> Number of previous, current selected restraints: 8624 12772 
    5784 make_re_417_> Restraint type to be calculated: DISTANCE 
    5785  
    5786 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3361215 3282.437
    5787 3.206 
    5788 make_re_422_> Number of previous, current restraints : 13005 17440 
    5789 make_re_423_> Number of previous, current selected restraints: 12772 17207 
    5790 make_re_417_> Restraint type to be calculated: DISTANCE 
    5791  
    5792 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3885503 3794.437
    5793 3.706 
    5794 make_re_422_> Number of previous, current restraints : 17440 21486 
    5795 make_re_423_> Number of previous, current selected restraints: 17207 21253 
    5796 make_re_417_> Restraint type to be calculated: DISTANCE 
    5797  
    5798 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4147647 4050.437
    5799 3.956 
    5800 make_re_422_> Number of previous, current restraints : 21486 23455 
    5801 make_re_423_> Number of previous, current selected restraints: 21253 23222 
    5802 0 atoms in HETATM/BLK residues constrained 
    5803 to protein atoms within 2.30 angstroms 
    5804 and protein CA atoms within 10.00 angstroms 
    5805 make_re_417_> Restraint type to be calculated: DISTANCE 
    5806 make_re_422_> Number of previous, current restraints : 23455 23455 
    5807 make_re_423_> Number of previous, current selected restraints: 23222 23222 
    5808 make_re_417_> Restraint type to be calculated: DISTANCE 
    5809 make_re_422_> Number of previous, current restraints : 23455 23455 
    5810 make_re_423_> Number of previous, current selected restraints: 23222 23222 
    5811 make_re_417_> Restraint type to be calculated: DISTANCE 
    5812 make_re_422_> Number of previous, current restraints : 23455 23455 
    5813 make_re_423_> Number of previous, current selected restraints: 23222 23222 
    5814 make_re_417_> Restraint type to be calculated: DISTANCE 
    5815 make_re_422_> Number of previous, current restraints : 23455 23455 
    5816 make_re_423_> Number of previous, current selected restraints: 23222 23222 
    5817 0 atoms in residues without defined topology 
    5818 constrained to be rigid bodies 
    5819 make_re_417_> Restraint type to be calculated: DISTANCE 
    5820 make_re_422_> Number of previous, current restraints : 23455 23455 
    5821 make_re_423_> Number of previous, current selected restraints: 23222 23222 
    5822 rmdupl__427_> 1360 redundant cosine dihedral restraints were unselected. 
    5823 condens_443_> Restraints marked for deletion were removed. 
    5824 Total number of restraints before, now: 23455 21862 
    5825 openf___224_> Open chain_W.rsr 
    5826 openf___224_> Open chain_W.rsr 
    5827  
    5828 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4260279 4160.429
    5829 4.063 
    5830 rdcsr2__307_> Number of restraints read : 21862 
    5831 Number of excluded pairs read: 0 
    5832 Number of pseudo atoms read : 0 
    5833 rdcsrs__304_> Restraints in memory, selected restraints: 21862 21862 
    5834 Explicitly excluded atom pairs in memory : 0 
    5835 Pseudo atoms in memory : 0 
    5836  
    5837 No output models from Modeller; see log for Modeller text output. 
    5838 Modeller job (ID LTL1YE68ZN1VUUVV) finished 
    5839  
    5840 Modeller error output 
    5841 Traceback (most recent call last): 
    5842 File "ModellerModelling.py", line 93, in   
    5843 a.make() 
    5844 File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
    5845 line 42, in make 
    5846 AutoModel.make(self, exit_stage) 
    5847 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    5848 line 151, in make 
    5849 atmsel = self._check_select_atoms() 
    5850 File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
    5851 line 700, in _check_select_atoms 
    5852 raise ModellerError("no atoms selected for optimization") 
    5853 _modeller.ModellerError: no atoms selected for optimization 
    5854  
    5855  
    5856 Modeller run output 
    5857  
    5858 MODELLER 10.6, 2024/10/17, r12888 
    5859  
    5860 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 
    5861  
    5862  
    5863 Copyright(c) 1989-2024 Andrej Sali 
    5864 All Rights Reserved 
    5865  
    5866 Written by A. Sali 
    5867 with help from 
    5868 B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 
    5869 M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, 
    5870 A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, 
    5871 F. Melo, J.P. Overington, E. Feyfant 
    5872 University of California, San Francisco, USA 
    5873 Rockefeller University, New York, USA 
    5874 Harvard University, Cambridge, USA 
    5875 Imperial Cancer Research Fund, London, UK 
    5876 Birkbeck College, University of London, London, UK 
    5877  
    5878  
    5879 Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
    5880 4.18.0-553.44.1.el8_10.x86_64 x86_64 
    5881 Date and time of compilation : 2024/10/17 20:43:03 
    5882 MODELLER executable type : x86_64-intel8 
    5883 Job starting time (YY/MM/DD HH:MM:SS): 2025/04/03 10:33:45 
    5884  
    5885 environ____W> The class 'environ' is deprecated; use 'Environ' instead 
    5886 openf___224_> Open $(LIB)/restyp.lib 
    5887 openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib 
    5888 rdresgr_266_> Number of residue groups: 2 
    5889 openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib 
    5890  
    5891 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
    5892 0.183 
    5893  
    5894 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
    5895 0.183 
    5896 openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib 
    5897  
    5898 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
    5899 0.230 
    5900 rdrdih__263_> Number of dihedral angle types : 9 
    5901 Maximal number of dihedral angle optima: 3 
    5902 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 
    5903 openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib 
    5904  
    5905 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
    5906 0.242 
    5907 openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib 
    5908 rdwilmo_274_> Mainchain residue conformation classes: APBLE 
    5909 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib 
    5910 rdclass_257_> Number of classes: 5 
    5911 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib 
    5912 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib 
    5913 openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib 
    5914 openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat 
    5915 rdrrwgh_268_> Number of residue types: 21 
    5916 dope_loopm_W> The class 'dope_loopmodel' is deprecated; use 'DOPELoopModel'
    5917 instead 
    5918 openf___224_> Open alignment.ali 
    5919  
    5920 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
    5921 0.270 
    5922  
    5923 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
    5924 0.284 
    5925  
    5926 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
    5927 0.299 
    5928  
    5929 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
    5930 0.328 
    5931  
    5932 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
    5933 0.387 
    5934  
    5935 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405537 396.032 0.387 
    5936  
    5937 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405565 396.060 0.387 
    5938  
    5939 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406477 396.950 0.388 
    5940  
    5941 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 407389 397.841 0.389 
    5942  
    5943 Read the alignment from file : alignment.ali 
    5944  
    5945 Total number of alignment positions: 229 
     1308[deleted to fit within ticket limits]
     1309
    59461310 
    59471311# Code #_Res #_Segm PDB_code Name