Sun 23 Dec 22:23:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmf-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:18 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 326 and 0 Target number of residues in the AU: 326 Target solvent content: 0.6119 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 67.531 3.400 Wilson plot Bfac: 57.67 6666 reflections ( 99.72 % complete ) and 0 restraints for refining 3849 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2996 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2681 (Rfree = 0.000) for 3849 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3933 seeds are put forward NCS extension: 0 residues added, 3933 seeds are put forward Round 1: 218 peptides, 39 chains. Longest chain 14 peptides. Score 0.404 Round 2: 282 peptides, 38 chains. Longest chain 15 peptides. Score 0.608 Round 3: 304 peptides, 34 chains. Longest chain 21 peptides. Score 0.699 Round 4: 312 peptides, 28 chains. Longest chain 28 peptides. Score 0.765 Round 5: 307 peptides, 29 chains. Longest chain 30 peptides. Score 0.749 Taking the results from Round 4 Chains 31, Residues 284, Estimated correctness of the model 73.1 % 3 chains (50 residues) have been docked in sequence Building loops using Loopy2018 31 chains (284 residues) following loop building 3 chains (50 residues) in sequence following loop building ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6246 restraints for refining 3160 atoms. 4996 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2528 (Rfree = 0.000) for 3160 atoms. Found 16 (23 requested) and removed 19 (11 requested) atoms. Cycle 2: After refmac, R = 0.2472 (Rfree = 0.000) for 3115 atoms. Found 9 (23 requested) and removed 16 (11 requested) atoms. Cycle 3: After refmac, R = 0.2272 (Rfree = 0.000) for 3084 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 4: After refmac, R = 0.2190 (Rfree = 0.000) for 3070 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 5: After refmac, R = 0.2166 (Rfree = 0.000) for 3058 atoms. Found 4 (21 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3174 seeds are put forward NCS extension: 26 residues added (12 deleted due to clashes), 3200 seeds are put forward Round 1: 255 peptides, 34 chains. Longest chain 19 peptides. Score 0.584 Round 2: 290 peptides, 31 chains. Longest chain 25 peptides. Score 0.699 Round 3: 305 peptides, 29 chains. Longest chain 25 peptides. Score 0.745 Round 4: 290 peptides, 29 chains. Longest chain 25 peptides. Score 0.718 Round 5: 293 peptides, 28 chains. Longest chain 29 peptides. Score 0.732 Taking the results from Round 3 Chains 29, Residues 276, Estimated correctness of the model 68.7 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6726 restraints for refining 3163 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2296 (Rfree = 0.000) for 3163 atoms. Found 10 (21 requested) and removed 17 (11 requested) atoms. Cycle 7: After refmac, R = 0.2250 (Rfree = 0.000) for 3146 atoms. Found 12 (20 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 3137 atoms. Found 12 (20 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.2343 (Rfree = 0.000) for 3129 atoms. Found 14 (19 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.2252 (Rfree = 0.000) for 3124 atoms. Found 3 (19 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 3245 seeds are put forward Round 1: 283 peptides, 38 chains. Longest chain 22 peptides. Score 0.611 Round 2: 307 peptides, 32 chains. Longest chain 25 peptides. Score 0.723 Round 3: 316 peptides, 29 chains. Longest chain 35 peptides. Score 0.764 Round 4: 306 peptides, 32 chains. Longest chain 28 peptides. Score 0.721 Round 5: 295 peptides, 31 chains. Longest chain 33 peptides. Score 0.709 Taking the results from Round 3 Chains 31, Residues 287, Estimated correctness of the model 72.8 % 2 chains (44 residues) have been docked in sequence Building loops using Loopy2018 31 chains (287 residues) following loop building 2 chains (44 residues) in sequence following loop building ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6529 restraints for refining 3163 atoms. 5256 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2443 (Rfree = 0.000) for 3163 atoms. Found 13 (18 requested) and removed 24 (11 requested) atoms. Cycle 12: After refmac, R = 0.2291 (Rfree = 0.000) for 3141 atoms. Found 13 (18 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2214 (Rfree = 0.000) for 3138 atoms. Found 6 (17 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2168 (Rfree = 0.000) for 3133 atoms. Found 1 (17 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2134 (Rfree = 0.000) for 3122 atoms. Found 2 (17 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3224 seeds are put forward Round 1: 274 peptides, 37 chains. Longest chain 18 peptides. Score 0.599 Round 2: 301 peptides, 33 chains. Longest chain 23 peptides. Score 0.703 Round 3: 295 peptides, 33 chains. Longest chain 23 peptides. Score 0.690 Round 4: 298 peptides, 31 chains. Longest chain 24 peptides. Score 0.715 Round 5: 293 peptides, 32 chains. Longest chain 31 peptides. Score 0.696 Taking the results from Round 4 Chains 31, Residues 267, Estimated correctness of the model 61.6 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6824 restraints for refining 3163 atoms. 5731 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2281 (Rfree = 0.000) for 3163 atoms. Found 14 (16 requested) and removed 20 (11 requested) atoms. Cycle 17: After refmac, R = 0.2147 (Rfree = 0.000) for 3149 atoms. Found 5 (16 requested) and removed 12 (11 requested) atoms. Cycle 18: After refmac, R = 0.2078 (Rfree = 0.000) for 3139 atoms. Found 4 (15 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2025 (Rfree = 0.000) for 3128 atoms. Found 3 (15 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 3114 atoms. Found 9 (14 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3236 seeds are put forward Round 1: 240 peptides, 35 chains. Longest chain 25 peptides. Score 0.530 Round 2: 273 peptides, 32 chains. Longest chain 26 peptides. Score 0.652 Round 3: 280 peptides, 28 chains. Longest chain 40 peptides. Score 0.707 Round 4: 279 peptides, 30 chains. Longest chain 28 peptides. Score 0.686 Round 5: 288 peptides, 30 chains. Longest chain 32 peptides. Score 0.705 Taking the results from Round 3 Chains 31, Residues 252, Estimated correctness of the model 59.7 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 31 chains (252 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6719 restraints for refining 3164 atoms. 5594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2219 (Rfree = 0.000) for 3164 atoms. Found 14 (14 requested) and removed 16 (11 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 3153 atoms. Found 6 (13 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.2013 (Rfree = 0.000) for 3140 atoms. Found 5 (13 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.1973 (Rfree = 0.000) for 3130 atoms. Found 5 (12 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2017 (Rfree = 0.000) for 3123 atoms. Found 4 (12 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3197 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 3235 seeds are put forward Round 1: 237 peptides, 34 chains. Longest chain 38 peptides. Score 0.534 Round 2: 252 peptides, 33 chains. Longest chain 26 peptides. Score 0.588 Round 3: 264 peptides, 31 chains. Longest chain 30 peptides. Score 0.642 Round 4: 261 peptides, 29 chains. Longest chain 40 peptides. Score 0.656 Round 5: 262 peptides, 33 chains. Longest chain 24 peptides. Score 0.614 Taking the results from Round 4 Chains 32, Residues 232, Estimated correctness of the model 45.9 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6850 restraints for refining 3164 atoms. 5825 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2192 (Rfree = 0.000) for 3164 atoms. Found 11 (11 requested) and removed 17 (11 requested) atoms. Cycle 27: After refmac, R = 0.2083 (Rfree = 0.000) for 3151 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 28: After refmac, R = 0.2068 (Rfree = 0.000) for 3145 atoms. Found 8 (11 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1988 (Rfree = 0.000) for 3135 atoms. Found 11 (11 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.1923 (Rfree = 0.000) for 3128 atoms. Found 7 (11 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 3207 seeds are put forward NCS extension: 33 residues added (8 deleted due to clashes), 3240 seeds are put forward Round 1: 220 peptides, 34 chains. Longest chain 22 peptides. Score 0.482 Round 2: 243 peptides, 32 chains. Longest chain 22 peptides. Score 0.576 Round 3: 243 peptides, 30 chains. Longest chain 30 peptides. Score 0.600 Round 4: 257 peptides, 33 chains. Longest chain 30 peptides. Score 0.601 Round 5: 234 peptides, 29 chains. Longest chain 30 peptides. Score 0.588 Taking the results from Round 4 Chains 34, Residues 224, Estimated correctness of the model 29.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6736 restraints for refining 3164 atoms. 5733 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2254 (Rfree = 0.000) for 3164 atoms. Found 11 (11 requested) and removed 18 (11 requested) atoms. Cycle 32: After refmac, R = 0.2321 (Rfree = 0.000) for 3138 atoms. Found 11 (11 requested) and removed 17 (11 requested) atoms. Cycle 33: After refmac, R = 0.2122 (Rfree = 0.000) for 3126 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 3119 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2043 (Rfree = 0.000) for 3115 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 3255 seeds are put forward Round 1: 215 peptides, 33 chains. Longest chain 14 peptides. Score 0.480 Round 2: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.527 Round 3: 212 peptides, 28 chains. Longest chain 26 peptides. Score 0.539 Round 4: 215 peptides, 31 chains. Longest chain 16 peptides. Score 0.508 Round 5: 212 peptides, 30 chains. Longest chain 16 peptides. Score 0.512 Taking the results from Round 3 Chains 28, Residues 184, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7400 restraints for refining 3163 atoms. 6692 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2065 (Rfree = 0.000) for 3163 atoms. Found 10 (11 requested) and removed 11 (11 requested) atoms. Cycle 37: After refmac, R = 0.1956 (Rfree = 0.000) for 3158 atoms. Found 10 (11 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2083 (Rfree = 0.000) for 3154 atoms. Found 11 (11 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.1987 (Rfree = 0.000) for 3148 atoms. Found 8 (11 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.1787 (Rfree = 0.000) for 3138 atoms. Found 3 (11 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 3204 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 3241 seeds are put forward Round 1: 188 peptides, 31 chains. Longest chain 13 peptides. Score 0.419 Round 2: 205 peptides, 26 chains. Longest chain 26 peptides. Score 0.545 Round 3: 220 peptides, 28 chains. Longest chain 15 peptides. Score 0.562 Round 4: 224 peptides, 30 chains. Longest chain 15 peptides. Score 0.548 Round 5: 216 peptides, 29 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 3 Chains 28, Residues 192, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7130 restraints for refining 3120 atoms. 6390 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2041 (Rfree = 0.000) for 3120 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.2297 (Rfree = 0.000) for 3115 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.2162 (Rfree = 0.000) for 3109 atoms. Found 11 (11 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.2250 (Rfree = 0.000) for 3101 atoms. Found 11 (11 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.1984 (Rfree = 0.000) for 3091 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 3165 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3179 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 12 peptides. Score 0.390 Round 2: 211 peptides, 29 chains. Longest chain 20 peptides. Score 0.522 Round 3: 219 peptides, 32 chains. Longest chain 19 peptides. Score 0.506 Round 4: 208 peptides, 27 chains. Longest chain 22 peptides. Score 0.540 Round 5: 207 peptides, 30 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 181, Estimated correctness of the model 7.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6666 reflections ( 99.72 % complete ) and 7210 restraints for refining 3143 atoms. 6513 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2202 (Rfree = 0.000) for 3143 atoms. Found 0 (11 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 3123 atoms. Found 0 (11 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1964 (Rfree = 0.000) for 3111 atoms. Found 0 (11 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1913 (Rfree = 0.000) for 3097 atoms. Found 0 (11 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 55.1