null Sun 23 Dec 22:23:07 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 1vr3-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.4-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/1vr3-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.4-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 22:23:17 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/1vr3-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-3.4-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 245 and 0 Target number of residues in the AU: 245 Target solvent content: 0.6289 Checking the provided sequence file Detected sequence length: 191 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 191 Adjusted target solvent content: 0.71 Input MTZ file: 1vr3-3.4-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: 92 Cell parameters: 79.137 79.137 114.115 90.000 90.000 90.000 Input sequence file: 1vr3-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1528 target number of atoms Had to go as low as 1.10 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: 65.030 3.400 Wilson plot Bfac: 65.95 5353 reflections ( 99.74 % complete ) and 0 restraints for refining 1702 atoms. Observations/parameters ratio is 0.79 ------------------------------------------------------ Starting model: R = 0.3374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.39 Search for helices and strands: 0 residues in 0 chains, 1733 seeds are put forward Round 1: 130 peptides, 15 chains. Longest chain 20 peptides. Score 0.522 Round 2: 133 peptides, 11 chains. Longest chain 26 peptides. Score 0.605 Round 3: 141 peptides, 11 chains. Longest chain 31 peptides. Score 0.632 Round 4: 132 peptides, 15 chains. Longest chain 23 peptides. Score 0.530 Round 5: 136 peptides, 12 chains. Longest chain 38 peptides. Score 0.598 Taking the results from Round 3 Chains 11, Residues 130, Estimated correctness of the model 38.8 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2797 restraints for refining 1566 atoms. 2061 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 1566 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 2: After refmac, R = 0.2628 (Rfree = 0.000) for 1526 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.2623 (Rfree = 0.000) for 1502 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2520 (Rfree = 0.000) for 1502 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2668 (Rfree = 0.000) for 1496 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.42 Search for helices and strands: 0 residues in 0 chains, 1534 seeds are put forward Round 1: 141 peptides, 17 chains. Longest chain 21 peptides. Score 0.529 Round 2: 141 peptides, 11 chains. Longest chain 51 peptides. Score 0.632 Round 3: 131 peptides, 13 chains. Longest chain 40 peptides. Score 0.562 Round 4: 129 peptides, 14 chains. Longest chain 21 peptides. Score 0.537 Round 5: 141 peptides, 12 chains. Longest chain 22 peptides. Score 0.615 Taking the results from Round 2 Chains 11, Residues 130, Estimated correctness of the model 38.8 % 1 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2462 restraints for refining 1448 atoms. 1699 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2824 (Rfree = 0.000) for 1448 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 7: After refmac, R = 0.2548 (Rfree = 0.000) for 1412 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 1401 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2304 (Rfree = 0.000) for 1390 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2238 (Rfree = 0.000) for 1390 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 1442 seeds are put forward Round 1: 145 peptides, 13 chains. Longest chain 31 peptides. Score 0.612 Round 2: 147 peptides, 12 chains. Longest chain 30 peptides. Score 0.635 Round 3: 143 peptides, 15 chains. Longest chain 29 peptides. Score 0.571 Round 4: 141 peptides, 11 chains. Longest chain 49 peptides. Score 0.632 Round 5: 133 peptides, 13 chains. Longest chain 29 peptides. Score 0.570 Taking the results from Round 2 Chains 14, Residues 135, Estimated correctness of the model 39.7 % 3 chains (60 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2451 restraints for refining 1438 atoms. 1655 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2609 (Rfree = 0.000) for 1438 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 12: After refmac, R = 0.2722 (Rfree = 0.000) for 1422 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.2473 (Rfree = 0.000) for 1414 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 14: After refmac, R = 0.2260 (Rfree = 0.000) for 1404 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2603 (Rfree = 0.000) for 1402 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 1438 seeds are put forward Round 1: 142 peptides, 14 chains. Longest chain 35 peptides. Score 0.585 Round 2: 146 peptides, 13 chains. Longest chain 25 peptides. Score 0.616 Round 3: 146 peptides, 14 chains. Longest chain 26 peptides. Score 0.599 Round 4: 147 peptides, 13 chains. Longest chain 50 peptides. Score 0.619 Round 5: 151 peptides, 10 chains. Longest chain 50 peptides. Score 0.679 Taking the results from Round 5 Chains 11, Residues 141, Estimated correctness of the model 52.3 % 1 chains (45 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2373 restraints for refining 1389 atoms. 1616 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2741 (Rfree = 0.000) for 1389 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2620 (Rfree = 0.000) for 1369 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2459 (Rfree = 0.000) for 1365 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2366 (Rfree = 0.000) for 1358 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2269 (Rfree = 0.000) for 1351 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 2.40 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward Round 1: 136 peptides, 11 chains. Longest chain 40 peptides. Score 0.615 Round 2: 140 peptides, 8 chains. Longest chain 53 peptides. Score 0.677 Round 3: 144 peptides, 11 chains. Longest chain 51 peptides. Score 0.642 Round 4: 138 peptides, 11 chains. Longest chain 43 peptides. Score 0.622 Round 5: 152 peptides, 10 chains. Longest chain 49 peptides. Score 0.682 Taking the results from Round 5 Chains 12, Residues 142, Estimated correctness of the model 53.1 % 2 chains (71 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2103 restraints for refining 1389 atoms. 1207 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2740 (Rfree = 0.000) for 1389 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.2500 (Rfree = 0.000) for 1375 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2350 (Rfree = 0.000) for 1366 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2202 (Rfree = 0.000) for 1363 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.2277 (Rfree = 0.000) for 1354 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 1409 seeds are put forward Round 1: 143 peptides, 10 chains. Longest chain 43 peptides. Score 0.654 Round 2: 150 peptides, 10 chains. Longest chain 43 peptides. Score 0.676 Round 3: 149 peptides, 15 chains. Longest chain 51 peptides. Score 0.593 Round 4: 145 peptides, 11 chains. Longest chain 39 peptides. Score 0.645 Round 5: 149 peptides, 13 chains. Longest chain 51 peptides. Score 0.626 Taking the results from Round 2 Chains 10, Residues 140, Estimated correctness of the model 51.5 % 2 chains (68 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2142 restraints for refining 1389 atoms. 1280 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2715 (Rfree = 0.000) for 1389 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2432 (Rfree = 0.000) for 1377 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.2482 (Rfree = 0.000) for 1376 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 29: After refmac, R = 0.2235 (Rfree = 0.000) for 1372 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2207 (Rfree = 0.000) for 1370 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.42 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward Round 1: 147 peptides, 14 chains. Longest chain 27 peptides. Score 0.603 Round 2: 149 peptides, 8 chains. Longest chain 61 peptides. Score 0.702 Round 3: 140 peptides, 13 chains. Longest chain 27 peptides. Score 0.595 Round 4: 151 peptides, 10 chains. Longest chain 39 peptides. Score 0.679 Round 5: 139 peptides, 12 chains. Longest chain 31 peptides. Score 0.609 Taking the results from Round 2 Chains 8, Residues 141, Estimated correctness of the model 58.4 % 2 chains (99 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 113 A 6 chains (142 residues) following loop building 1 chains (104 residues) in sequence following loop building ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 1919 restraints for refining 1469 atoms. 853 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2955 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 33 (5 requested) atoms. Cycle 32: After refmac, R = 0.2784 (Rfree = 0.000) for 1433 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2581 (Rfree = 0.000) for 1429 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2557 (Rfree = 0.000) for 1418 atoms. Found 7 (9 requested) and removed 16 (5 requested) atoms. Cycle 35: After refmac, R = 0.2387 (Rfree = 0.000) for 1407 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.35 Search for helices and strands: 0 residues in 0 chains, 1447 seeds are put forward Round 1: 142 peptides, 12 chains. Longest chain 39 peptides. Score 0.619 Round 2: 147 peptides, 7 chains. Longest chain 62 peptides. Score 0.712 Round 3: 145 peptides, 8 chains. Longest chain 57 peptides. Score 0.691 Round 4: 137 peptides, 12 chains. Longest chain 51 peptides. Score 0.602 Round 5: 135 peptides, 13 chains. Longest chain 28 peptides. Score 0.577 Taking the results from Round 2 Chains 9, Residues 140, Estimated correctness of the model 60.9 % 2 chains (71 residues) have been docked in sequence Building loops using Loopy2018 9 chains (140 residues) following loop building 2 chains (71 residues) in sequence following loop building ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2167 restraints for refining 1390 atoms. 1270 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2785 (Rfree = 0.000) for 1390 atoms. Found 9 (9 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2407 (Rfree = 0.000) for 1380 atoms. Found 9 (9 requested) and removed 18 (5 requested) atoms. Cycle 38: After refmac, R = 0.2240 (Rfree = 0.000) for 1368 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2100 (Rfree = 0.000) for 1366 atoms. Found 8 (8 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2070 (Rfree = 0.000) for 1365 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.38 Search for helices and strands: 0 residues in 0 chains, 1395 seeds are put forward Round 1: 137 peptides, 12 chains. Longest chain 33 peptides. Score 0.602 Round 2: 139 peptides, 12 chains. Longest chain 27 peptides. Score 0.609 Round 3: 142 peptides, 11 chains. Longest chain 25 peptides. Score 0.635 Round 4: 140 peptides, 11 chains. Longest chain 37 peptides. Score 0.629 Round 5: 143 peptides, 8 chains. Longest chain 48 peptides. Score 0.685 Taking the results from Round 5 Chains 8, Residues 135, Estimated correctness of the model 53.9 % 2 chains (74 residues) have been docked in sequence ------------------------------------------------------ 5353 reflections ( 99.74 % complete ) and 2116 restraints for refining 1389 atoms. 1223 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2450 (Rfree = 0.000) for 1389 atoms. Found 8 (8 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2383 (Rfree = 0.000) for 1379 atoms. Found 8 (8 requested) and removed 20 (5 requested) atoms. Cycle 43: After refmac, R = 0.2397 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 15 (5 requested) atoms. Cycle 44: After refmac, R = 0.2375 (Rfree = 0.000) for 1352 atoms. Found 8 (8 requested) and removed 14 (5 requested) atoms. Cycle 45: After refmac, R = 0.2025 (Rfree = 0.000) for 1344 atoms. Found 8 (8 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 1384 seeds are put forward Round 1: 143 peptides, 14 chains. Longest chain 31 peptides. Score 0.589 Round 2: 137 peptides, 7 chains. Longest chain 51 peptides. Score 0.683 Round 3: 134 peptides, 13 chains. Longest chain 24 peptides. Score 0.574 Round 4: 146 peptides, 10 chains. Longest chain 43 peptides. Score 0.664 Round 5: 141 peptides, 12 chains. Longest chain 31 peptides. Score 0.615 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 130, Estimated correctness of the model 53.4 % 4 chains (103 residues) have been docked in sequence Sequence coverage is 78 % Consider running further cycles of model building using 1vr3-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 82 A and 91 A Built loop between residues 140 A and 153 A 5 chains (147 residues) following loop building 2 chains (123 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5353 reflections ( 99.74 % complete ) and 1843 restraints for refining 1487 atoms. 677 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2548 (Rfree = 0.000) for 1487 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2334 (Rfree = 0.000) for 1475 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2244 (Rfree = 0.000) for 1468 atoms. Found 0 (9 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2266 (Rfree = 0.000) for 1467 atoms. Found 0 (9 requested) and removed 1 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:57:01 GMT 2018 Job finished. TimeTaking 33.9 Used memory is bytes: 17206312