Mon 24 Dec 00:17:20 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkn-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:18:35 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.6-parrot-mrncs/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 974 and 0 Target number of residues in the AU: 974 Target solvent content: 0.6408 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.6-parrot-mrncs.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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.75 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: 93.562 3.600 Wilson plot Bfac: 72.40 16761 reflections ( 98.94 % complete ) and 0 restraints for refining 12427 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3051 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2609 (Rfree = 0.000) for 12427 atoms. Found 79 (79 requested) and removed 72 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 12648 seeds are put forward NCS extension: 0 residues added, 12648 seeds are put forward Round 1: 646 peptides, 117 chains. Longest chain 14 peptides. Score 0.383 Round 2: 772 peptides, 109 chains. Longest chain 18 peptides. Score 0.543 Round 3: 816 peptides, 108 chains. Longest chain 23 peptides. Score 0.585 Round 4: 827 peptides, 97 chains. Longest chain 24 peptides. Score 0.633 Round 5: 856 peptides, 106 chains. Longest chain 27 peptides. Score 0.624 Taking the results from Round 4 Chains 103, Residues 730, Estimated correctness of the model 27.1 % 9 chains (81 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22131 restraints for refining 10178 atoms. 19023 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2096 (Rfree = 0.000) for 10178 atoms. Found 62 (65 requested) and removed 63 (32 requested) atoms. Cycle 2: After refmac, R = 0.1951 (Rfree = 0.000) for 10043 atoms. Found 31 (65 requested) and removed 49 (32 requested) atoms. Cycle 3: After refmac, R = 0.1878 (Rfree = 0.000) for 9979 atoms. Found 27 (64 requested) and removed 49 (32 requested) atoms. Cycle 4: After refmac, R = 0.1768 (Rfree = 0.000) for 9925 atoms. Found 21 (63 requested) and removed 43 (31 requested) atoms. Cycle 5: After refmac, R = 0.1716 (Rfree = 0.000) for 9886 atoms. Found 18 (63 requested) and removed 43 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10177 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 10194 seeds are put forward Round 1: 742 peptides, 115 chains. Longest chain 20 peptides. Score 0.491 Round 2: 838 peptides, 102 chains. Longest chain 21 peptides. Score 0.624 Round 3: 840 peptides, 102 chains. Longest chain 26 peptides. Score 0.626 Round 4: 856 peptides, 103 chains. Longest chain 32 peptides. Score 0.634 Round 5: 874 peptides, 107 chains. Longest chain 30 peptides. Score 0.634 Taking the results from Round 5 Chains 112, Residues 767, Estimated correctness of the model 27.5 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22456 restraints for refining 10181 atoms. 19363 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2157 (Rfree = 0.000) for 10181 atoms. Found 58 (65 requested) and removed 57 (32 requested) atoms. Cycle 7: After refmac, R = 0.1938 (Rfree = 0.000) for 10097 atoms. Found 46 (65 requested) and removed 45 (32 requested) atoms. Cycle 8: After refmac, R = 0.1877 (Rfree = 0.000) for 10051 atoms. Found 38 (64 requested) and removed 41 (32 requested) atoms. Cycle 9: After refmac, R = 0.1802 (Rfree = 0.000) for 10023 atoms. Found 33 (64 requested) and removed 42 (32 requested) atoms. Cycle 10: After refmac, R = 0.1756 (Rfree = 0.000) for 9994 atoms. Found 39 (64 requested) and removed 44 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 10312 seeds are put forward NCS extension: 21 residues added (16 deleted due to clashes), 10333 seeds are put forward Round 1: 700 peptides, 108 chains. Longest chain 19 peptides. Score 0.480 Round 2: 776 peptides, 97 chains. Longest chain 30 peptides. Score 0.593 Round 3: 787 peptides, 98 chains. Longest chain 23 peptides. Score 0.598 Round 4: 784 peptides, 94 chains. Longest chain 30 peptides. Score 0.610 Round 5: 795 peptides, 93 chains. Longest chain 25 peptides. Score 0.623 Taking the results from Round 5 Chains 98, Residues 702, Estimated correctness of the model 23.4 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23065 restraints for refining 10180 atoms. 20226 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2021 (Rfree = 0.000) for 10180 atoms. Found 53 (65 requested) and removed 58 (32 requested) atoms. Cycle 12: After refmac, R = 0.1805 (Rfree = 0.000) for 10113 atoms. Found 34 (65 requested) and removed 46 (32 requested) atoms. Cycle 13: After refmac, R = 0.1761 (Rfree = 0.000) for 10071 atoms. Found 38 (64 requested) and removed 39 (32 requested) atoms. Cycle 14: After refmac, R = 0.1654 (Rfree = 0.000) for 10048 atoms. Found 42 (64 requested) and removed 40 (32 requested) atoms. Cycle 15: After refmac, R = 0.1698 (Rfree = 0.000) for 10037 atoms. Found 40 (64 requested) and removed 42 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 10354 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 10368 seeds are put forward Round 1: 733 peptides, 121 chains. Longest chain 18 peptides. Score 0.456 Round 2: 788 peptides, 106 chains. Longest chain 21 peptides. Score 0.569 Round 3: 783 peptides, 106 chains. Longest chain 23 peptides. Score 0.565 Round 4: 795 peptides, 98 chains. Longest chain 27 peptides. Score 0.605 Round 5: 816 peptides, 101 chains. Longest chain 30 peptides. Score 0.611 Taking the results from Round 5 Chains 104, Residues 715, Estimated correctness of the model 18.9 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22733 restraints for refining 10181 atoms. 19759 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1955 (Rfree = 0.000) for 10181 atoms. Found 45 (65 requested) and removed 51 (32 requested) atoms. Cycle 17: After refmac, R = 0.1829 (Rfree = 0.000) for 10119 atoms. Found 37 (65 requested) and removed 37 (32 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1725 (Rfree = 0.000) for 10076 atoms. Found 31 (64 requested) and removed 36 (32 requested) atoms. Cycle 19: After refmac, R = 0.1685 (Rfree = 0.000) for 10050 atoms. Found 22 (64 requested) and removed 42 (32 requested) atoms. Cycle 20: After refmac, R = 0.1615 (Rfree = 0.000) for 10017 atoms. Found 20 (64 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10309 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 10343 seeds are put forward Round 1: 696 peptides, 122 chains. Longest chain 14 peptides. Score 0.414 Round 2: 760 peptides, 110 chains. Longest chain 24 peptides. Score 0.528 Round 3: 767 peptides, 106 chains. Longest chain 23 peptides. Score 0.551 Round 4: 792 peptides, 104 chains. Longest chain 30 peptides. Score 0.580 Round 5: 801 peptides, 106 chains. Longest chain 26 peptides. Score 0.580 Taking the results from Round 5 Chains 108, Residues 695, Estimated correctness of the model 6.7 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22361 restraints for refining 10181 atoms. 19407 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2016 (Rfree = 0.000) for 10181 atoms. Found 60 (65 requested) and removed 59 (32 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1817 (Rfree = 0.000) for 10122 atoms. Found 32 (65 requested) and removed 45 (32 requested) atoms. Cycle 23: After refmac, R = 0.1741 (Rfree = 0.000) for 10072 atoms. Found 28 (64 requested) and removed 43 (32 requested) atoms. Cycle 24: After refmac, R = 0.1681 (Rfree = 0.000) for 10028 atoms. Found 35 (64 requested) and removed 39 (32 requested) atoms. Cycle 25: After refmac, R = 0.1619 (Rfree = 0.000) for 10007 atoms. Found 31 (64 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 10316 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10336 seeds are put forward Round 1: 651 peptides, 118 chains. Longest chain 16 peptides. Score 0.383 Round 2: 703 peptides, 108 chains. Longest chain 20 peptides. Score 0.482 Round 3: 716 peptides, 106 chains. Longest chain 18 peptides. Score 0.504 Round 4: 738 peptides, 106 chains. Longest chain 22 peptides. Score 0.524 Round 5: 704 peptides, 108 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 4 Chains 109, Residues 632, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23766 restraints for refining 10181 atoms. 21280 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1848 (Rfree = 0.000) for 10181 atoms. Found 65 (65 requested) and removed 44 (32 requested) atoms. Cycle 27: After refmac, R = 0.1713 (Rfree = 0.000) for 10161 atoms. Found 48 (65 requested) and removed 43 (32 requested) atoms. Cycle 28: After refmac, R = 0.1637 (Rfree = 0.000) for 10141 atoms. Found 39 (65 requested) and removed 39 (32 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1594 (Rfree = 0.000) for 10119 atoms. Found 54 (65 requested) and removed 40 (32 requested) atoms. Cycle 30: After refmac, R = 0.1553 (Rfree = 0.000) for 10127 atoms. Found 36 (65 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 10448 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 10476 seeds are put forward Round 1: 575 peptides, 105 chains. Longest chain 16 peptides. Score 0.360 Round 2: 657 peptides, 104 chains. Longest chain 28 peptides. Score 0.454 Round 3: 648 peptides, 101 chains. Longest chain 21 peptides. Score 0.458 Round 4: 670 peptides, 101 chains. Longest chain 26 peptides. Score 0.480 Round 5: 685 peptides, 104 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 5 Chains 104, Residues 581, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23648 restraints for refining 10181 atoms. 21375 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1837 (Rfree = 0.000) for 10181 atoms. Found 52 (65 requested) and removed 41 (32 requested) atoms. Cycle 32: After refmac, R = 0.1704 (Rfree = 0.000) for 10156 atoms. Found 33 (65 requested) and removed 37 (32 requested) atoms. Cycle 33: After refmac, R = 0.1716 (Rfree = 0.000) for 10135 atoms. Found 38 (65 requested) and removed 42 (32 requested) atoms. Cycle 34: After refmac, R = 0.1614 (Rfree = 0.000) for 10115 atoms. Found 35 (64 requested) and removed 39 (32 requested) atoms. Cycle 35: After refmac, R = 0.1608 (Rfree = 0.000) for 10095 atoms. Found 35 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 10388 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 10417 seeds are put forward Round 1: 556 peptides, 106 chains. Longest chain 12 peptides. Score 0.334 Round 2: 632 peptides, 100 chains. Longest chain 21 peptides. Score 0.446 Round 3: 656 peptides, 100 chains. Longest chain 22 peptides. Score 0.471 Round 4: 672 peptides, 102 chains. Longest chain 17 peptides. Score 0.478 Round 5: 672 peptides, 100 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 5 Chains 101, Residues 572, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23631 restraints for refining 10182 atoms. 21368 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1798 (Rfree = 0.000) for 10182 atoms. Found 60 (65 requested) and removed 43 (32 requested) atoms. Cycle 37: After refmac, R = 0.1669 (Rfree = 0.000) for 10170 atoms. Found 42 (65 requested) and removed 40 (32 requested) atoms. Cycle 38: After refmac, R = 0.1657 (Rfree = 0.000) for 10151 atoms. Found 58 (65 requested) and removed 42 (32 requested) atoms. Cycle 39: After refmac, R = 0.1564 (Rfree = 0.000) for 10160 atoms. Found 39 (65 requested) and removed 37 (32 requested) atoms. Cycle 40: After refmac, R = 0.1558 (Rfree = 0.000) for 10155 atoms. Found 43 (65 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 10445 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 10468 seeds are put forward Round 1: 574 peptides, 110 chains. Longest chain 15 peptides. Score 0.335 Round 2: 601 peptides, 101 chains. Longest chain 21 peptides. Score 0.409 Round 3: 649 peptides, 104 chains. Longest chain 24 peptides. Score 0.446 Round 4: 613 peptides, 94 chains. Longest chain 22 peptides. Score 0.454 Round 5: 617 peptides, 96 chains. Longest chain 22 peptides. Score 0.449 Taking the results from Round 4 Chains 94, Residues 519, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23997 restraints for refining 10182 atoms. 21913 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1780 (Rfree = 0.000) for 10182 atoms. Found 55 (65 requested) and removed 38 (32 requested) atoms. Cycle 42: After refmac, R = 0.1763 (Rfree = 0.000) for 10167 atoms. Found 65 (65 requested) and removed 38 (32 requested) atoms. Cycle 43: After refmac, R = 0.1660 (Rfree = 0.000) for 10179 atoms. Found 55 (65 requested) and removed 41 (32 requested) atoms. Cycle 44: After refmac, R = 0.1651 (Rfree = 0.000) for 10180 atoms. Found 50 (65 requested) and removed 35 (32 requested) atoms. Cycle 45: After refmac, R = 0.1602 (Rfree = 0.000) for 10184 atoms. Found 50 (65 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10460 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 10471 seeds are put forward Round 1: 516 peptides, 104 chains. Longest chain 12 peptides. Score 0.296 Round 2: 596 peptides, 103 chains. Longest chain 15 peptides. Score 0.394 Round 3: 589 peptides, 96 chains. Longest chain 21 peptides. Score 0.419 Round 4: 587 peptides, 93 chains. Longest chain 16 peptides. Score 0.431 Round 5: 591 peptides, 93 chains. Longest chain 15 peptides. Score 0.435 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 93, Residues 498, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 93 chains (498 residues) following loop building 3 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16761 reflections ( 98.94 % complete ) and 24037 restraints for refining 10181 atoms. 22093 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1756 (Rfree = 0.000) for 10181 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1750 (Rfree = 0.000) for 10117 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1735 (Rfree = 0.000) for 10068 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1682 (Rfree = 0.000) for 10010 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Writing output files ... TimeTaking 227.62