null Tue 25 Dec 19:27:57 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 1vk9-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.2-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/1vk9-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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/1vk9-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-3.2-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 227 and 0 Target number of residues in the AU: 227 Target solvent content: 0.6372 Checking the provided sequence file Detected sequence length: 151 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 302 Adjusted target solvent content: 0.52 Input MTZ file: 1vk9-3.2-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.40 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: 115.114 3.200 Wilson plot Bfac: 70.20 6074 reflections ( 99.95 % complete ) and 0 restraints for refining 2682 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3071 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3345 (Rfree = 0.000) for 2682 atoms. Found 23 (23 requested) and removed 53 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 2677 seeds are put forward NCS extension: 0 residues added, 2677 seeds are put forward Round 1: 102 peptides, 13 chains. Longest chain 20 peptides. Score 0.453 Round 2: 115 peptides, 11 chains. Longest chain 22 peptides. Score 0.551 Round 3: 121 peptides, 11 chains. Longest chain 42 peptides. Score 0.575 Round 4: 116 peptides, 11 chains. Longest chain 31 peptides. Score 0.555 Round 5: 111 peptides, 12 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 3 Chains 12, Residues 110, Estimated correctness of the model 34.1 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 4708 restraints for refining 2040 atoms. 4173 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2740 (Rfree = 0.000) for 2040 atoms. Found 18 (18 requested) and removed 58 (9 requested) atoms. Cycle 2: After refmac, R = 0.2804 (Rfree = 0.000) for 1902 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2730 (Rfree = 0.000) for 1872 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2684 (Rfree = 0.000) for 1861 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2687 (Rfree = 0.000) for 1842 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 1881 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 1904 seeds are put forward Round 1: 130 peptides, 14 chains. Longest chain 18 peptides. Score 0.554 Round 2: 131 peptides, 11 chains. Longest chain 37 peptides. Score 0.612 Round 3: 129 peptides, 15 chains. Longest chain 17 peptides. Score 0.531 Round 4: 136 peptides, 13 chains. Longest chain 21 peptides. Score 0.595 Round 5: 132 peptides, 12 chains. Longest chain 20 peptides. Score 0.598 Taking the results from Round 2 Chains 11, Residues 120, Estimated correctness of the model 44.3 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 3318 restraints for refining 1695 atoms. 2691 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2612 (Rfree = 0.000) for 1695 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 7: After refmac, R = 0.2478 (Rfree = 0.000) for 1661 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 8: After refmac, R = 0.2420 (Rfree = 0.000) for 1648 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 9: After refmac, R = 0.2407 (Rfree = 0.000) for 1633 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2341 (Rfree = 0.000) for 1632 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1673 seeds are put forward NCS extension: 51 residues added (5 deleted due to clashes), 1724 seeds are put forward Round 1: 131 peptides, 12 chains. Longest chain 30 peptides. Score 0.594 Round 2: 135 peptides, 9 chains. Longest chain 47 peptides. Score 0.660 Round 3: 139 peptides, 14 chains. Longest chain 31 peptides. Score 0.588 Round 4: 129 peptides, 11 chains. Longest chain 25 peptides. Score 0.605 Round 5: 131 peptides, 9 chains. Longest chain 30 peptides. Score 0.647 Taking the results from Round 2 Chains 9, Residues 126, Estimated correctness of the model 56.2 % 1 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2836 restraints for refining 1551 atoms. 2152 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2600 (Rfree = 0.000) for 1551 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 12: After refmac, R = 0.2327 (Rfree = 0.000) for 1526 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.2388 (Rfree = 0.000) for 1516 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2311 (Rfree = 0.000) for 1512 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2228 (Rfree = 0.000) for 1506 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 1542 seeds are put forward NCS extension: 61 residues added (5 deleted due to clashes), 1603 seeds are put forward Round 1: 138 peptides, 11 chains. Longest chain 57 peptides. Score 0.637 Round 2: 141 peptides, 7 chains. Longest chain 68 peptides. Score 0.710 Round 3: 134 peptides, 7 chains. Longest chain 42 peptides. Score 0.690 Round 4: 138 peptides, 11 chains. Longest chain 40 peptides. Score 0.637 Round 5: 138 peptides, 11 chains. Longest chain 24 peptides. Score 0.637 Taking the results from Round 2 Chains 9, Residues 134, Estimated correctness of the model 67.3 % 2 chains (88 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 122 A 7 chains (136 residues) following loop building 1 chains (93 residues) in sequence following loop building ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2273 restraints for refining 1550 atoms. 1356 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2393 (Rfree = 0.000) for 1550 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 17: After refmac, R = 0.2637 (Rfree = 0.000) for 1522 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 18: After refmac, R = 0.2169 (Rfree = 0.000) for 1492 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.2158 (Rfree = 0.000) for 1481 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2513 (Rfree = 0.000) for 1483 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1502 seeds are put forward NCS extension: 164 residues added (6 deleted due to clashes), 1666 seeds are put forward Round 1: 130 peptides, 11 chains. Longest chain 40 peptides. Score 0.609 Round 2: 140 peptides, 8 chains. Longest chain 54 peptides. Score 0.692 Round 3: 137 peptides, 9 chains. Longest chain 59 peptides. Score 0.667 Round 4: 140 peptides, 9 chains. Longest chain 78 peptides. Score 0.676 Round 5: 125 peptides, 12 chains. Longest chain 20 peptides. Score 0.572 Taking the results from Round 2 Chains 8, Residues 132, Estimated correctness of the model 63.5 % 2 chains (77 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2440 restraints for refining 1516 atoms. 1603 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2252 (Rfree = 0.000) for 1516 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 22: After refmac, R = 0.2624 (Rfree = 0.000) for 1508 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 23: After refmac, R = 0.2459 (Rfree = 0.000) for 1492 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2068 (Rfree = 0.000) for 1486 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2086 (Rfree = 0.000) for 1490 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward NCS extension: 0 residues added, 1517 seeds are put forward Round 1: 137 peptides, 11 chains. Longest chain 39 peptides. Score 0.633 Round 2: 144 peptides, 12 chains. Longest chain 39 peptides. Score 0.640 Round 3: 141 peptides, 11 chains. Longest chain 65 peptides. Score 0.647 Round 4: 138 peptides, 10 chains. Longest chain 46 peptides. Score 0.653 Round 5: 133 peptides, 10 chains. Longest chain 41 peptides. Score 0.637 Taking the results from Round 4 Chains 14, Residues 128, Estimated correctness of the model 54.6 % 4 chains (90 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2419 restraints for refining 1573 atoms. 1545 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2768 (Rfree = 0.000) for 1573 atoms. Found 13 (13 requested) and removed 36 (7 requested) atoms. Cycle 27: After refmac, R = 0.2670 (Rfree = 0.000) for 1539 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.2512 (Rfree = 0.000) for 1524 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2564 (Rfree = 0.000) for 1517 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.2531 (Rfree = 0.000) for 1513 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 1533 seeds are put forward NCS extension: 0 residues added, 1533 seeds are put forward Round 1: 127 peptides, 11 chains. Longest chain 38 peptides. Score 0.598 Round 2: 139 peptides, 10 chains. Longest chain 28 peptides. Score 0.657 Round 3: 123 peptides, 11 chains. Longest chain 35 peptides. Score 0.583 Round 4: 131 peptides, 11 chains. Longest chain 26 peptides. Score 0.612 Round 5: 125 peptides, 13 chains. Longest chain 16 peptides. Score 0.553 Taking the results from Round 2 Chains 11, Residues 129, Estimated correctness of the model 55.5 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2612 restraints for refining 1507 atoms. 1865 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2692 (Rfree = 0.000) for 1507 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 32: After refmac, R = 0.2276 (Rfree = 0.000) for 1487 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.2350 (Rfree = 0.000) for 1480 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2186 (Rfree = 0.000) for 1476 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2417 (Rfree = 0.000) for 1473 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.11 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 1538 seeds are put forward Round 1: 134 peptides, 10 chains. Longest chain 38 peptides. Score 0.640 Round 2: 137 peptides, 9 chains. Longest chain 26 peptides. Score 0.667 Round 3: 140 peptides, 8 chains. Longest chain 41 peptides. Score 0.692 Round 4: 144 peptides, 9 chains. Longest chain 28 peptides. Score 0.688 Round 5: 138 peptides, 9 chains. Longest chain 40 peptides. Score 0.670 Taking the results from Round 3 Chains 10, Residues 132, Estimated correctness of the model 63.5 % 3 chains (82 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2309 restraints for refining 1517 atoms. 1441 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2454 (Rfree = 0.000) for 1517 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 37: After refmac, R = 0.2578 (Rfree = 0.000) for 1497 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.2138 (Rfree = 0.000) for 1483 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2102 (Rfree = 0.000) for 1472 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2254 (Rfree = 0.000) for 1469 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 0 residues added, 1486 seeds are put forward Round 1: 128 peptides, 11 chains. Longest chain 42 peptides. Score 0.601 Round 2: 138 peptides, 8 chains. Longest chain 68 peptides. Score 0.686 Round 3: 131 peptides, 6 chains. Longest chain 51 peptides. Score 0.697 Round 4: 128 peptides, 7 chains. Longest chain 40 peptides. Score 0.671 Round 5: 131 peptides, 8 chains. Longest chain 47 peptides. Score 0.664 Taking the results from Round 3 Chains 6, Residues 125, Estimated correctness of the model 64.5 % 2 chains (76 residues) have been docked in sequence ------------------------------------------------------ 6074 reflections ( 99.95 % complete ) and 2350 restraints for refining 1490 atoms. 1541 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2081 (Rfree = 0.000) for 1490 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 42: After refmac, R = 0.1879 (Rfree = 0.000) for 1480 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 43: After refmac, R = 0.1812 (Rfree = 0.000) for 1475 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1751 (Rfree = 0.000) for 1470 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1666 (Rfree = 0.000) for 1467 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 1478 seeds are put forward NCS extension: 0 residues added, 1478 seeds are put forward Round 1: 132 peptides, 9 chains. Longest chain 54 peptides. Score 0.650 Round 2: 138 peptides, 9 chains. Longest chain 27 peptides. Score 0.670 Round 3: 135 peptides, 5 chains. Longest chain 46 peptides. Score 0.724 Round 4: 128 peptides, 12 chains. Longest chain 24 peptides. Score 0.583 Round 5: 130 peptides, 9 chains. Longest chain 29 peptides. Score 0.644 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 130, Estimated correctness of the model 70.1 % 4 chains (124 residues) have been docked in sequence Sequence coverage is 94 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 45 A and 49 A Built loop between residues 93 A and 102 A Built loop between residues 116 A and 122 A 2 chains (145 residues) following loop building 1 chains (140 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 6074 reflections ( 99.95 % complete ) and 1167 restraints for refining 1144 atoms. Observations/parameters ratio is 1.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3230 (Rfree = 0.000) for 1144 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 47: After refmac, R = 0.2847 (Rfree = 0.000) for 1144 atoms. Found 3 (9 requested) and removed 1 (5 requested) atoms. Cycle 48: After refmac, R = 0.2675 (Rfree = 0.000) for 1144 atoms. Found 8 (9 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2517 (Rfree = 0.000) for 1144 atoms. Found 7 (9 requested) and removed 1 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:18:16 GMT 2018 Job finished. TimeTaking 50.31 Used memory is bytes: 19826928