null Sun 23 Dec 22:22:41 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 1vk9-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.6-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/1vk9-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.6-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 22:22:51 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/1vk9-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.6-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 216 and 0 Target number of residues in the AU: 216 Target solvent content: 0.6547 Checking the provided sequence file Detected sequence length: 151 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 151 Adjusted target solvent content: 0.76 Input MTZ file: 1vk9-3.6-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1208 target number of atoms Had to go as low as 1.35 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: 115.114 3.600 Wilson plot Bfac: 81.31 4327 reflections ( 99.93 % complete ) and 0 restraints for refining 1340 atoms. Observations/parameters ratio is 0.81 ------------------------------------------------------ Starting model: R = 0.3645 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3494 (Rfree = 0.000) for 1340 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 2.44 Search for helices and strands: 0 residues in 0 chains, 1348 seeds are put forward Round 1: 97 peptides, 12 chains. Longest chain 17 peptides. Score 0.452 Round 2: 110 peptides, 11 chains. Longest chain 25 peptides. Score 0.531 Round 3: 101 peptides, 12 chains. Longest chain 22 peptides. Score 0.470 Round 4: 108 peptides, 11 chains. Longest chain 27 peptides. Score 0.522 Round 5: 112 peptides, 9 chains. Longest chain 24 peptides. Score 0.579 Taking the results from Round 5 Chains 9, Residues 103, Estimated correctness of the model 6.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2279 restraints for refining 1101 atoms. 1876 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3068 (Rfree = 0.000) for 1101 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2919 (Rfree = 0.000) for 1092 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.2821 (Rfree = 0.000) for 1085 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2841 (Rfree = 0.000) for 1088 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2785 (Rfree = 0.000) for 1086 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 2.40 Search for helices and strands: 0 residues in 0 chains, 1151 seeds are put forward Round 1: 115 peptides, 12 chains. Longest chain 20 peptides. Score 0.531 Round 2: 107 peptides, 11 chains. Longest chain 28 peptides. Score 0.518 Round 3: 115 peptides, 8 chains. Longest chain 29 peptides. Score 0.609 Round 4: 116 peptides, 11 chains. Longest chain 27 peptides. Score 0.555 Round 5: 111 peptides, 8 chains. Longest chain 39 peptides. Score 0.594 Taking the results from Round 3 Chains 8, Residues 107, Estimated correctness of the model 18.1 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2184 restraints for refining 1095 atoms. 1746 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2733 (Rfree = 0.000) for 1095 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 7: After refmac, R = 0.2627 (Rfree = 0.000) for 1090 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2548 (Rfree = 0.000) for 1084 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.2531 (Rfree = 0.000) for 1084 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2604 (Rfree = 0.000) for 1081 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 2.45 Search for helices and strands: 0 residues in 0 chains, 1125 seeds are put forward Round 1: 106 peptides, 11 chains. Longest chain 24 peptides. Score 0.514 Round 2: 111 peptides, 11 chains. Longest chain 21 peptides. Score 0.535 Round 3: 101 peptides, 11 chains. Longest chain 25 peptides. Score 0.492 Round 4: 107 peptides, 11 chains. Longest chain 18 peptides. Score 0.518 Round 5: 104 peptides, 12 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 2 Chains 11, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2323 restraints for refining 1095 atoms. 1934 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2679 (Rfree = 0.000) for 1095 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 12: After refmac, R = 0.2572 (Rfree = 0.000) for 1091 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2458 (Rfree = 0.000) for 1092 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.2455 (Rfree = 0.000) for 1094 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2496 (Rfree = 0.000) for 1093 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.40 Search for helices and strands: 0 residues in 0 chains, 1148 seeds are put forward Round 1: 108 peptides, 11 chains. Longest chain 21 peptides. Score 0.522 Round 2: 114 peptides, 9 chains. Longest chain 22 peptides. Score 0.586 Round 3: 114 peptides, 8 chains. Longest chain 23 peptides. Score 0.605 Round 4: 108 peptides, 10 chains. Longest chain 22 peptides. Score 0.543 Round 5: 106 peptides, 9 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 3 Chains 9, Residues 106, Estimated correctness of the model 16.6 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2130 restraints for refining 1100 atoms. 1648 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2745 (Rfree = 0.000) for 1100 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2516 (Rfree = 0.000) for 1092 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.2488 (Rfree = 0.000) for 1089 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2436 (Rfree = 0.000) for 1089 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2406 (Rfree = 0.000) for 1090 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 2.42 Search for helices and strands: 0 residues in 0 chains, 1132 seeds are put forward Round 1: 114 peptides, 13 chains. Longest chain 23 peptides. Score 0.507 Round 2: 118 peptides, 11 chains. Longest chain 26 peptides. Score 0.563 Round 3: 118 peptides, 9 chains. Longest chain 38 peptides. Score 0.601 Round 4: 121 peptides, 9 chains. Longest chain 27 peptides. Score 0.612 Round 5: 116 peptides, 11 chains. Longest chain 22 peptides. Score 0.555 Taking the results from Round 4 Chains 9, Residues 112, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2279 restraints for refining 1101 atoms. 1840 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2657 (Rfree = 0.000) for 1101 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.2562 (Rfree = 0.000) for 1097 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2510 (Rfree = 0.000) for 1098 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2505 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2557 (Rfree = 0.000) for 1101 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 2.42 Search for helices and strands: 0 residues in 0 chains, 1149 seeds are put forward Round 1: 109 peptides, 11 chains. Longest chain 29 peptides. Score 0.527 Round 2: 108 peptides, 11 chains. Longest chain 28 peptides. Score 0.522 Round 3: 117 peptides, 10 chains. Longest chain 43 peptides. Score 0.579 Round 4: 118 peptides, 12 chains. Longest chain 19 peptides. Score 0.544 Round 5: 121 peptides, 11 chains. Longest chain 25 peptides. Score 0.575 Taking the results from Round 3 Chains 10, Residues 107, Estimated correctness of the model 6.3 % 1 chains (42 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 1912 restraints for refining 1145 atoms. 1317 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2741 (Rfree = 0.000) for 1145 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 27: After refmac, R = 0.2680 (Rfree = 0.000) for 1128 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2530 (Rfree = 0.000) for 1125 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2494 (Rfree = 0.000) for 1125 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2489 (Rfree = 0.000) for 1128 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 2.45 Search for helices and strands: 0 residues in 0 chains, 1193 seeds are put forward Round 1: 101 peptides, 14 chains. Longest chain 16 peptides. Score 0.426 Round 2: 103 peptides, 13 chains. Longest chain 18 peptides. Score 0.458 Round 3: 111 peptides, 13 chains. Longest chain 18 peptides. Score 0.494 Round 4: 113 peptides, 11 chains. Longest chain 26 peptides. Score 0.543 Round 5: 116 peptides, 12 chains. Longest chain 19 peptides. Score 0.536 Taking the results from Round 4 Chains 12, Residues 102, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 2113 restraints for refining 1099 atoms. 1621 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2776 (Rfree = 0.000) for 1099 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2517 (Rfree = 0.000) for 1094 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2476 (Rfree = 0.000) for 1095 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2465 (Rfree = 0.000) for 1097 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2407 (Rfree = 0.000) for 1098 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 2.44 Search for helices and strands: 0 residues in 0 chains, 1148 seeds are put forward Round 1: 113 peptides, 9 chains. Longest chain 23 peptides. Score 0.582 Round 2: 117 peptides, 6 chains. Longest chain 38 peptides. Score 0.653 Round 3: 124 peptides, 6 chains. Longest chain 42 peptides. Score 0.675 Round 4: 116 peptides, 9 chains. Longest chain 36 peptides. Score 0.594 Round 5: 109 peptides, 10 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 3 Chains 6, Residues 118, Estimated correctness of the model 41.6 % 1 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 1847 restraints for refining 1127 atoms. 1200 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2578 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2393 (Rfree = 0.000) for 1124 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2390 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2296 (Rfree = 0.000) for 1123 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2386 (Rfree = 0.000) for 1124 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 2.40 Search for helices and strands: 0 residues in 0 chains, 1165 seeds are put forward Round 1: 106 peptides, 12 chains. Longest chain 18 peptides. Score 0.493 Round 2: 113 peptides, 8 chains. Longest chain 51 peptides. Score 0.602 Round 3: 112 peptides, 9 chains. Longest chain 31 peptides. Score 0.579 Round 4: 109 peptides, 11 chains. Longest chain 30 peptides. Score 0.527 Round 5: 112 peptides, 9 chains. Longest chain 31 peptides. Score 0.579 Taking the results from Round 2 Chains 8, Residues 105, Estimated correctness of the model 15.4 % 1 chains (50 residues) have been docked in sequence ------------------------------------------------------ 4327 reflections ( 99.93 % complete ) and 1966 restraints for refining 1130 atoms. 1355 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2541 (Rfree = 0.000) for 1130 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2353 (Rfree = 0.000) for 1126 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2299 (Rfree = 0.000) for 1125 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.2157 (Rfree = 0.000) for 1123 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.2174 (Rfree = 0.000) for 1122 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 2.42 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 106 peptides, 10 chains. Longest chain 21 peptides. Score 0.534 Round 2: 116 peptides, 8 chains. Longest chain 34 peptides. Score 0.613 Round 3: 109 peptides, 10 chains. Longest chain 20 peptides. Score 0.547 Round 4: 112 peptides, 11 chains. Longest chain 23 peptides. Score 0.539 Round 5: 114 peptides, 9 chains. Longest chain 25 peptides. Score 0.586 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 108, Estimated correctness of the model 19.7 % 1 chains (33 residues) have been docked in sequence Sequence coverage is 30 % Consider running further cycles of model building using 1vk9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4327 reflections ( 99.93 % complete ) and 1938 restraints for refining 1114 atoms. 1369 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2395 (Rfree = 0.000) for 1114 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2419 (Rfree = 0.000) for 1107 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2364 (Rfree = 0.000) for 1099 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2327 (Rfree = 0.000) for 1094 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:12 GMT 2018 Job finished. TimeTaking 32.53 Used memory is bytes: 720232