null Sun 23 Dec 22:23:10 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 2oh3-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.2-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/2oh3-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.2-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 22:23:19 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/2oh3-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-3.2-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 148 and 0 Target number of residues in the AU: 148 Target solvent content: 0.6318 Checking the provided sequence file Detected sequence length: 167 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 167 Adjusted target solvent content: 0.58 Input MTZ file: 2oh3-3.2-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: 23 Cell parameters: 64.360 75.280 89.790 90.000 90.000 90.000 Input sequence file: 2oh3-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1336 target number of atoms Had to go as low as 0.70 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: 57.688 3.200 Wilson plot Bfac: 66.42 3738 reflections ( 97.93 % complete ) and 0 restraints for refining 1489 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3309 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2538 (Rfree = 0.000) for 1489 atoms. Found 11 (13 requested) and removed 62 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 1481 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 13 peptides. Score 0.375 Round 2: 109 peptides, 13 chains. Longest chain 26 peptides. Score 0.595 Round 3: 123 peptides, 14 chains. Longest chain 31 peptides. Score 0.645 Round 4: 123 peptides, 15 chains. Longest chain 18 peptides. Score 0.621 Round 5: 112 peptides, 13 chains. Longest chain 19 peptides. Score 0.611 Taking the results from Round 3 Chains 14, Residues 109, Estimated correctness of the model 52.6 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2293 restraints for refining 1220 atoms. 1733 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2875 (Rfree = 0.000) for 1220 atoms. Found 10 (10 requested) and removed 35 (5 requested) atoms. Cycle 2: After refmac, R = 0.2797 (Rfree = 0.000) for 1173 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2739 (Rfree = 0.000) for 1163 atoms. Found 4 (10 requested) and removed 13 (5 requested) atoms. Cycle 4: After refmac, R = 0.2693 (Rfree = 0.000) for 1152 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2619 (Rfree = 0.000) for 1147 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 116 peptides, 12 chains. Longest chain 34 peptides. Score 0.656 Round 2: 115 peptides, 11 chains. Longest chain 33 peptides. Score 0.674 Round 3: 130 peptides, 8 chains. Longest chain 40 peptides. Score 0.792 Round 4: 121 peptides, 11 chains. Longest chain 31 peptides. Score 0.701 Round 5: 120 peptides, 10 chains. Longest chain 39 peptides. Score 0.717 Taking the results from Round 3 Chains 10, Residues 122, Estimated correctness of the model 82.2 % 2 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 47 A 8 chains (123 residues) following loop building 1 chains (73 residues) in sequence following loop building ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 1762 restraints for refining 1218 atoms. 958 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2879 (Rfree = 0.000) for 1218 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2774 (Rfree = 0.000) for 1200 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.2741 (Rfree = 0.000) for 1178 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2654 (Rfree = 0.000) for 1173 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2674 (Rfree = 0.000) for 1168 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.77 Search for helices and strands: 0 residues in 0 chains, 1212 seeds are put forward Round 1: 115 peptides, 13 chains. Longest chain 20 peptides. Score 0.627 Round 2: 127 peptides, 9 chains. Longest chain 49 peptides. Score 0.764 Round 3: 130 peptides, 11 chains. Longest chain 22 peptides. Score 0.738 Round 4: 124 peptides, 13 chains. Longest chain 29 peptides. Score 0.672 Round 5: 127 peptides, 11 chains. Longest chain 26 peptides. Score 0.726 Taking the results from Round 2 Chains 10, Residues 118, Estimated correctness of the model 77.6 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 34 A 8 chains (118 residues) following loop building 1 chains (41 residues) in sequence following loop building ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 1982 restraints for refining 1147 atoms. 1411 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2978 (Rfree = 0.000) for 1147 atoms. Found 9 (9 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2830 (Rfree = 0.000) for 1134 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.2632 (Rfree = 0.000) for 1127 atoms. Found 9 (9 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.2536 (Rfree = 0.000) for 1121 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.2689 (Rfree = 0.000) for 1117 atoms. Found 8 (8 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 1172 seeds are put forward Round 1: 107 peptides, 11 chains. Longest chain 25 peptides. Score 0.634 Round 2: 115 peptides, 11 chains. Longest chain 23 peptides. Score 0.674 Round 3: 122 peptides, 10 chains. Longest chain 38 peptides. Score 0.726 Round 4: 128 peptides, 11 chains. Longest chain 27 peptides. Score 0.730 Round 5: 128 peptides, 11 chains. Longest chain 34 peptides. Score 0.730 Taking the results from Round 5 Chains 12, Residues 117, Estimated correctness of the model 71.3 % 2 chains (48 residues) have been docked in sequence Building loops using Loopy2018 12 chains (117 residues) following loop building 2 chains (48 residues) in sequence following loop building ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2098 restraints for refining 1220 atoms. 1462 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2917 (Rfree = 0.000) for 1220 atoms. Found 8 (8 requested) and removed 19 (5 requested) atoms. Cycle 17: After refmac, R = 0.2652 (Rfree = 0.000) for 1196 atoms. Found 8 (8 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2474 (Rfree = 0.000) for 1186 atoms. Found 8 (8 requested) and removed 13 (5 requested) atoms. Cycle 19: After refmac, R = 0.2213 (Rfree = 0.000) for 1177 atoms. Found 7 (7 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2147 (Rfree = 0.000) for 1175 atoms. Found 5 (7 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 1206 seeds are put forward Round 1: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.539 Round 2: 126 peptides, 13 chains. Longest chain 42 peptides. Score 0.681 Round 3: 128 peptides, 14 chains. Longest chain 23 peptides. Score 0.669 Round 4: 123 peptides, 12 chains. Longest chain 23 peptides. Score 0.689 Round 5: 124 peptides, 12 chains. Longest chain 32 peptides. Score 0.693 Taking the results from Round 5 Chains 12, Residues 112, Estimated correctness of the model 63.7 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2295 restraints for refining 1220 atoms. 1737 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2648 (Rfree = 0.000) for 1220 atoms. Found 7 (7 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.2476 (Rfree = 0.000) for 1210 atoms. Found 7 (7 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2388 (Rfree = 0.000) for 1201 atoms. Found 4 (7 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2330 (Rfree = 0.000) for 1197 atoms. Found 4 (7 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2308 (Rfree = 0.000) for 1193 atoms. Found 1 (7 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.75 Search for helices and strands: 0 residues in 0 chains, 1230 seeds are put forward Round 1: 108 peptides, 14 chains. Longest chain 17 peptides. Score 0.563 Round 2: 120 peptides, 13 chains. Longest chain 25 peptides. Score 0.652 Round 3: 127 peptides, 12 chains. Longest chain 39 peptides. Score 0.706 Round 4: 118 peptides, 13 chains. Longest chain 26 peptides. Score 0.643 Round 5: 117 peptides, 13 chains. Longest chain 23 peptides. Score 0.637 Taking the results from Round 3 Chains 12, Residues 115, Estimated correctness of the model 66.4 % 3 chains (56 residues) have been docked in sequence Building loops using Loopy2018 12 chains (115 residues) following loop building 3 chains (56 residues) in sequence following loop building ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 1977 restraints for refining 1219 atoms. 1302 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2713 (Rfree = 0.000) for 1219 atoms. Found 7 (7 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2560 (Rfree = 0.000) for 1200 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2536 (Rfree = 0.000) for 1198 atoms. Found 7 (7 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.2440 (Rfree = 0.000) for 1195 atoms. Found 2 (6 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2397 (Rfree = 0.000) for 1189 atoms. Found 4 (6 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.90 Search for helices and strands: 0 residues in 0 chains, 1233 seeds are put forward Round 1: 93 peptides, 11 chains. Longest chain 18 peptides. Score 0.555 Round 2: 103 peptides, 13 chains. Longest chain 15 peptides. Score 0.560 Round 3: 116 peptides, 15 chains. Longest chain 16 peptides. Score 0.583 Round 4: 104 peptides, 12 chains. Longest chain 17 peptides. Score 0.592 Round 5: 110 peptides, 14 chains. Longest chain 16 peptides. Score 0.574 Taking the results from Round 4 Chains 12, Residues 92, Estimated correctness of the model 38.9 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2359 restraints for refining 1220 atoms. 1892 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2748 (Rfree = 0.000) for 1220 atoms. Found 6 (6 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2658 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2706 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2747 (Rfree = 0.000) for 1200 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2697 (Rfree = 0.000) for 1191 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 2.78 Search for helices and strands: 0 residues in 0 chains, 1231 seeds are put forward Round 1: 98 peptides, 14 chains. Longest chain 18 peptides. Score 0.500 Round 2: 107 peptides, 12 chains. Longest chain 26 peptides. Score 0.609 Round 3: 111 peptides, 12 chains. Longest chain 21 peptides. Score 0.630 Round 4: 117 peptides, 12 chains. Longest chain 32 peptides. Score 0.661 Round 5: 115 peptides, 12 chains. Longest chain 21 peptides. Score 0.651 Taking the results from Round 4 Chains 12, Residues 105, Estimated correctness of the model 56.5 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2135 restraints for refining 1220 atoms. 1551 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2787 (Rfree = 0.000) for 1220 atoms. Found 6 (6 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2721 (Rfree = 0.000) for 1207 atoms. Found 6 (6 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.2846 (Rfree = 0.000) for 1196 atoms. Found 6 (6 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.2578 (Rfree = 0.000) for 1187 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2396 (Rfree = 0.000) for 1183 atoms. Found 6 (6 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 1227 seeds are put forward Round 1: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.393 Round 2: 84 peptides, 11 chains. Longest chain 15 peptides. Score 0.497 Round 3: 93 peptides, 12 chains. Longest chain 15 peptides. Score 0.526 Round 4: 91 peptides, 12 chains. Longest chain 14 peptides. Score 0.513 Round 5: 88 peptides, 11 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 3 Chains 12, Residues 81, Estimated correctness of the model 19.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 97.93 % complete ) and 2840 restraints for refining 1220 atoms. 2528 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2481 (Rfree = 0.000) for 1220 atoms. Found 6 (6 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.2398 (Rfree = 0.000) for 1215 atoms. Found 6 (6 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2281 (Rfree = 0.000) for 1214 atoms. Found 6 (6 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2303 (Rfree = 0.000) for 1214 atoms. Found 4 (6 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2223 (Rfree = 0.000) for 1212 atoms. Found 4 (6 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 1244 seeds are put forward Round 1: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.429 Round 2: 93 peptides, 14 chains. Longest chain 13 peptides. Score 0.467 Round 3: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.487 Round 4: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.417 Round 5: 95 peptides, 13 chains. Longest chain 17 peptides. Score 0.510 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 82, Estimated correctness of the model 14.5 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2oh3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3738 reflections ( 97.93 % complete ) and 2586 restraints for refining 1220 atoms. 2221 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2602 (Rfree = 0.000) for 1220 atoms. Found 0 (6 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2495 (Rfree = 0.000) for 1212 atoms. Found 0 (6 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2487 (Rfree = 0.000) for 1205 atoms. Found 0 (6 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2609 (Rfree = 0.000) for 1199 atoms. Found 0 (6 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:16 GMT 2018 Job finished. TimeTaking 28.1 Used memory is bytes: 3683280