null Sun 23 Dec 22:23:02 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 1vjx-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.8-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/1vjx-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.8-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 22:23:12 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/1vjx-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-3.8-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 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.6586 Checking the provided sequence file Detected sequence length: 157 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 157 Adjusted target solvent content: 0.59 Input MTZ file: 1vjx-3.8-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: 98 Cell parameters: 82.326 82.326 121.618 90.000 90.000 90.000 Input sequence file: 1vjx-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1256 target number of atoms Had to go as low as 0.80 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 Loops will be built when appropriate and at the last cycle Resolution range: 68.175 3.800 Wilson plot Bfac: 83.18 2164 reflections ( 96.31 % complete ) and 0 restraints for refining 1401 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3628 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3418 (Rfree = 0.000) for 1401 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.28 Search for helices and strands: 0 residues in 0 chains, 1438 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.263 Round 2: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.413 Round 3: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.451 Round 4: 85 peptides, 12 chains. Longest chain 15 peptides. Score 0.484 Round 5: 89 peptides, 11 chains. Longest chain 17 peptides. Score 0.542 Taking the results from Round 5 Chains 11, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2630 restraints for refining 1135 atoms. 2329 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3048 (Rfree = 0.000) for 1135 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 2: After refmac, R = 0.2892 (Rfree = 0.000) for 1117 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2813 (Rfree = 0.000) for 1104 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2956 (Rfree = 0.000) for 1094 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 5: After refmac, R = 0.3146 (Rfree = 0.000) for 1072 atoms. Found 4 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.24 Search for helices and strands: 0 residues in 0 chains, 1131 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.329 Round 2: 93 peptides, 13 chains. Longest chain 22 peptides. Score 0.509 Round 3: 95 peptides, 10 chains. Longest chain 22 peptides. Score 0.608 Round 4: 89 peptides, 10 chains. Longest chain 15 peptides. Score 0.572 Round 5: 96 peptides, 12 chains. Longest chain 14 peptides. Score 0.558 Taking the results from Round 3 Chains 10, Residues 85, Estimated correctness of the model 2.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2327 restraints for refining 1077 atoms. 1997 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3055 (Rfree = 0.000) for 1077 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 7: After refmac, R = 0.2908 (Rfree = 0.000) for 1063 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2797 (Rfree = 0.000) for 1054 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2789 (Rfree = 0.000) for 1048 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.2722 (Rfree = 0.000) for 1041 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.28 Search for helices and strands: 0 residues in 0 chains, 1099 seeds are put forward Round 1: 80 peptides, 13 chains. Longest chain 13 peptides. Score 0.414 Round 2: 91 peptides, 13 chains. Longest chain 15 peptides. Score 0.495 Round 3: 86 peptides, 10 chains. Longest chain 19 peptides. Score 0.553 Round 4: 81 peptides, 10 chains. Longest chain 21 peptides. Score 0.520 Round 5: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.436 Taking the results from Round 3 Chains 10, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2448 restraints for refining 1088 atoms. 2154 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2823 (Rfree = 0.000) for 1088 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 12: After refmac, R = 0.2745 (Rfree = 0.000) for 1067 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2679 (Rfree = 0.000) for 1057 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2671 (Rfree = 0.000) for 1051 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2492 (Rfree = 0.000) for 1049 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.28 Search for helices and strands: 0 residues in 0 chains, 1112 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.303 Round 2: 86 peptides, 11 chains. Longest chain 16 peptides. Score 0.522 Round 3: 82 peptides, 12 chains. Longest chain 11 peptides. Score 0.463 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.433 Round 5: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 2 Chains 11, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2357 restraints for refining 1083 atoms. 2068 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2929 (Rfree = 0.000) for 1083 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.2679 (Rfree = 0.000) for 1064 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 18: After refmac, R = 0.2568 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 19: After refmac, R = 0.2529 (Rfree = 0.000) for 1054 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2576 (Rfree = 0.000) for 1052 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.30 Search for helices and strands: 0 residues in 0 chains, 1107 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 7 peptides. Score 0.342 Round 2: 69 peptides, 10 chains. Longest chain 14 peptides. Score 0.432 Round 3: 73 peptides, 9 chains. Longest chain 17 peptides. Score 0.496 Round 4: 80 peptides, 11 chains. Longest chain 17 peptides. Score 0.481 Round 5: 69 peptides, 9 chains. Longest chain 12 peptides. Score 0.467 Taking the results from Round 3 Chains 9, Residues 64, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2537 restraints for refining 1132 atoms. 2257 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2798 (Rfree = 0.000) for 1132 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2736 (Rfree = 0.000) for 1119 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2603 (Rfree = 0.000) for 1116 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2436 (Rfree = 0.000) for 1111 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2424 (Rfree = 0.000) for 1110 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.30 Search for helices and strands: 0 residues in 0 chains, 1171 seeds are put forward Round 1: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.350 Round 2: 73 peptides, 11 chains. Longest chain 16 peptides. Score 0.428 Round 3: 71 peptides, 10 chains. Longest chain 12 peptides. Score 0.448 Round 4: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.428 Round 5: 77 peptides, 11 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2733 restraints for refining 1135 atoms. 2480 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2817 (Rfree = 0.000) for 1135 atoms. Found 5 (6 requested) and removed 11 (3 requested) atoms. Cycle 27: After refmac, R = 0.2936 (Rfree = 0.000) for 1120 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2862 (Rfree = 0.000) for 1112 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 29: After refmac, R = 0.3059 (Rfree = 0.000) for 1102 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2731 (Rfree = 0.000) for 1090 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.31 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.238 Round 2: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.342 Round 3: 71 peptides, 11 chains. Longest chain 9 peptides. Score 0.413 Round 4: 69 peptides, 12 chains. Longest chain 8 peptides. Score 0.361 Round 5: 72 peptides, 12 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 3 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2546 restraints for refining 1105 atoms. 2317 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2773 (Rfree = 0.000) for 1105 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.2991 (Rfree = 0.000) for 1091 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2737 (Rfree = 0.000) for 1086 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 34: After refmac, R = 0.2829 (Rfree = 0.000) for 1078 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 35: After refmac, R = 0.2599 (Rfree = 0.000) for 1076 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.22 Search for helices and strands: 0 residues in 0 chains, 1129 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 9 peptides. Score 0.292 Round 2: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.389 Round 3: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.377 Round 4: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.421 Round 5: 75 peptides, 10 chains. Longest chain 23 peptides. Score 0.477 Taking the results from Round 5 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2376 restraints for refining 1135 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3054 (Rfree = 0.000) for 1135 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.3217 (Rfree = 0.000) for 1125 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.3049 (Rfree = 0.000) for 1113 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.2775 (Rfree = 0.000) for 1102 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.2526 (Rfree = 0.000) for 1092 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.30 Search for helices and strands: 0 residues in 0 chains, 1134 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.250 Round 2: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.368 Round 3: 66 peptides, 9 chains. Longest chain 11 peptides. Score 0.444 Round 4: 62 peptides, 9 chains. Longest chain 12 peptides. Score 0.413 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 3 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2164 reflections ( 96.31 % complete ) and 2537 restraints for refining 1081 atoms. 2318 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2927 (Rfree = 0.000) for 1081 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 42: After refmac, R = 0.2526 (Rfree = 0.000) for 1063 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.2472 (Rfree = 0.000) for 1064 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2446 (Rfree = 0.000) for 1065 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2587 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.27 Search for helices and strands: 0 residues in 0 chains, 1117 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.291 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.312 Round 3: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.342 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.327 Round 5: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2164 reflections ( 96.31 % complete ) and 2832 restraints for refining 1136 atoms. 2638 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3206 (Rfree = 0.000) for 1136 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3428 (Rfree = 0.000) for 1119 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3054 (Rfree = 0.000) for 1106 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2930 (Rfree = 0.000) for 1099 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:37 GMT 2018 Job finished. TimeTaking 27.59 Used memory is bytes: 233080