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 1vkn-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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/1vkn-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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 ============================================================ Tue 25 Dec 19:28:12 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/1vkn-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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 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-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.6-parrot-hancs.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 12487 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3065 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2649 (Rfree = 0.000) for 12487 atoms. Found 80 (80 requested) and removed 75 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 12724 seeds are put forward NCS extension: 0 residues added, 12724 seeds are put forward Round 1: 650 peptides, 109 chains. Longest chain 22 peptides. Score 0.424 Round 2: 779 peptides, 106 chains. Longest chain 26 peptides. Score 0.561 Round 3: 828 peptides, 109 chains. Longest chain 29 peptides. Score 0.591 Round 4: 841 peptides, 97 chains. Longest chain 29 peptides. Score 0.644 Round 5: 841 peptides, 96 chains. Longest chain 32 peptides. Score 0.647 Taking the results from Round 5 Chains 102, Residues 745, Estimated correctness of the model 32.1 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22028 restraints for refining 10174 atoms. 18835 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2211 (Rfree = 0.000) for 10174 atoms. Found 57 (65 requested) and removed 74 (32 requested) atoms. Cycle 2: After refmac, R = 0.2057 (Rfree = 0.000) for 10016 atoms. Found 47 (65 requested) and removed 49 (32 requested) atoms. Cycle 3: After refmac, R = 0.1987 (Rfree = 0.000) for 9935 atoms. Found 38 (64 requested) and removed 56 (32 requested) atoms. Cycle 4: After refmac, R = 0.1892 (Rfree = 0.000) for 9860 atoms. Found 43 (63 requested) and removed 39 (31 requested) atoms. Cycle 5: After refmac, R = 0.1884 (Rfree = 0.000) for 9830 atoms. Found 43 (63 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10225 seeds are put forward NCS extension: 14 residues added (12 deleted due to clashes), 10239 seeds are put forward Round 1: 714 peptides, 116 chains. Longest chain 17 peptides. Score 0.459 Round 2: 790 peptides, 109 chains. Longest chain 20 peptides. Score 0.559 Round 3: 812 peptides, 97 chains. Longest chain 29 peptides. Score 0.622 Round 4: 812 peptides, 96 chains. Longest chain 28 peptides. Score 0.625 Round 5: 839 peptides, 91 chains. Longest chain 29 peptides. Score 0.662 Taking the results from Round 5 Chains 96, Residues 748, Estimated correctness of the model 37.3 % 10 chains (109 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 21887 restraints for refining 10180 atoms. 18644 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2069 (Rfree = 0.000) for 10180 atoms. Found 55 (65 requested) and removed 61 (32 requested) atoms. Cycle 7: After refmac, R = 0.1941 (Rfree = 0.000) for 10088 atoms. Found 32 (65 requested) and removed 51 (32 requested) atoms. Cycle 8: After refmac, R = 0.1842 (Rfree = 0.000) for 10028 atoms. Found 21 (64 requested) and removed 39 (32 requested) atoms. Cycle 9: After refmac, R = 0.1826 (Rfree = 0.000) for 9981 atoms. Found 25 (64 requested) and removed 46 (32 requested) atoms. Cycle 10: After refmac, R = 0.1720 (Rfree = 0.000) for 9931 atoms. Found 28 (63 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 10237 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 10256 seeds are put forward Round 1: 734 peptides, 117 chains. Longest chain 16 peptides. Score 0.474 Round 2: 805 peptides, 111 chains. Longest chain 34 peptides. Score 0.564 Round 3: 827 peptides, 107 chains. Longest chain 30 peptides. Score 0.598 Round 4: 832 peptides, 101 chains. Longest chain 37 peptides. Score 0.623 Round 5: 830 peptides, 99 chains. Longest chain 24 peptides. Score 0.629 Taking the results from Round 5 Chains 103, Residues 731, Estimated correctness of the model 25.6 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22359 restraints for refining 10180 atoms. 19298 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2043 (Rfree = 0.000) for 10180 atoms. Found 52 (65 requested) and removed 53 (32 requested) atoms. Cycle 12: After refmac, R = 0.1876 (Rfree = 0.000) for 10114 atoms. Found 18 (65 requested) and removed 41 (32 requested) atoms. Cycle 13: After refmac, R = 0.1807 (Rfree = 0.000) for 10059 atoms. Found 20 (64 requested) and removed 37 (32 requested) atoms. Cycle 14: After refmac, R = 0.1780 (Rfree = 0.000) for 10019 atoms. Found 34 (64 requested) and removed 44 (32 requested) atoms. Cycle 15: After refmac, R = 0.1744 (Rfree = 0.000) for 9990 atoms. Found 35 (64 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10283 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 10306 seeds are put forward Round 1: 698 peptides, 121 chains. Longest chain 19 peptides. Score 0.420 Round 2: 771 peptides, 109 chains. Longest chain 20 peptides. Score 0.542 Round 3: 780 peptides, 107 chains. Longest chain 22 peptides. Score 0.558 Round 4: 782 peptides, 106 chains. Longest chain 23 peptides. Score 0.564 Round 5: 765 peptides, 104 chains. Longest chain 22 peptides. Score 0.557 Taking the results from Round 4 Chains 108, Residues 676, Estimated correctness of the model 0.1 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 22763 restraints for refining 10181 atoms. 19962 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1911 (Rfree = 0.000) for 10181 atoms. Found 49 (65 requested) and removed 54 (32 requested) atoms. Cycle 17: After refmac, R = 0.1720 (Rfree = 0.000) for 10106 atoms. Found 31 (65 requested) and removed 42 (32 requested) atoms. Cycle 18: After refmac, R = 0.1656 (Rfree = 0.000) for 10062 atoms. Found 29 (64 requested) and removed 35 (32 requested) atoms. Cycle 19: After refmac, R = 0.1636 (Rfree = 0.000) for 10029 atoms. Found 33 (64 requested) and removed 40 (32 requested) atoms. Cycle 20: After refmac, R = 0.1579 (Rfree = 0.000) for 9999 atoms. Found 30 (64 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10361 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10380 seeds are put forward Round 1: 644 peptides, 116 chains. Longest chain 16 peptides. Score 0.385 Round 2: 724 peptides, 107 chains. Longest chain 45 peptides. Score 0.507 Round 3: 733 peptides, 106 chains. Longest chain 21 peptides. Score 0.520 Round 4: 772 peptides, 111 chains. Longest chain 19 peptides. Score 0.535 Round 5: 750 peptides, 108 chains. Longest chain 25 peptides. Score 0.527 Taking the results from Round 4 Chains 112, Residues 661, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23017 restraints for refining 10179 atoms. 20397 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1926 (Rfree = 0.000) for 10179 atoms. Found 47 (65 requested) and removed 51 (32 requested) atoms. Cycle 22: After refmac, R = 0.1749 (Rfree = 0.000) for 10136 atoms. Found 22 (65 requested) and removed 40 (32 requested) atoms. Cycle 23: After refmac, R = 0.1672 (Rfree = 0.000) for 10098 atoms. Found 15 (64 requested) and removed 40 (32 requested) atoms. Cycle 24: After refmac, R = 0.1663 (Rfree = 0.000) for 10058 atoms. Found 13 (64 requested) and removed 36 (32 requested) atoms. Cycle 25: After refmac, R = 0.1585 (Rfree = 0.000) for 10021 atoms. Found 16 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10315 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 10329 seeds are put forward Round 1: 666 peptides, 114 chains. Longest chain 16 peptides. Score 0.418 Round 2: 718 peptides, 108 chains. Longest chain 18 peptides. Score 0.497 Round 3: 727 peptides, 104 chains. Longest chain 29 peptides. Score 0.522 Round 4: 738 peptides, 110 chains. Longest chain 33 peptides. Score 0.508 Round 5: 718 peptides, 111 chains. Longest chain 16 peptides. Score 0.484 Taking the results from Round 3 Chains 104, Residues 623, Estimated correctness of the model 0.0 % 7 chains (38 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23536 restraints for refining 10180 atoms. 21066 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1891 (Rfree = 0.000) for 10180 atoms. Found 56 (65 requested) and removed 42 (32 requested) atoms. Cycle 27: After refmac, R = 0.1737 (Rfree = 0.000) for 10162 atoms. Found 40 (65 requested) and removed 43 (32 requested) atoms. Cycle 28: After refmac, R = 0.1690 (Rfree = 0.000) for 10136 atoms. Found 39 (65 requested) and removed 36 (32 requested) atoms. Cycle 29: After refmac, R = 0.1614 (Rfree = 0.000) for 10118 atoms. Found 33 (65 requested) and removed 35 (32 requested) atoms. Cycle 30: After refmac, R = 0.1569 (Rfree = 0.000) for 10093 atoms. Found 25 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 10390 seeds are put forward NCS extension: 43 residues added (9 deleted due to clashes), 10433 seeds are put forward Round 1: 604 peptides, 114 chains. Longest chain 12 peptides. Score 0.350 Round 2: 684 peptides, 106 chains. Longest chain 19 peptides. Score 0.472 Round 3: 684 peptides, 102 chains. Longest chain 19 peptides. Score 0.490 Round 4: 704 peptides, 107 chains. Longest chain 35 peptides. Score 0.488 Round 5: 698 peptides, 102 chains. Longest chain 21 peptides. Score 0.503 Taking the results from Round 5 Chains 102, Residues 596, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23892 restraints for refining 10182 atoms. 21602 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1783 (Rfree = 0.000) for 10182 atoms. Found 57 (65 requested) and removed 40 (32 requested) atoms. Cycle 32: After refmac, R = 0.1703 (Rfree = 0.000) for 10159 atoms. Found 50 (65 requested) and removed 43 (32 requested) atoms. Cycle 33: After refmac, R = 0.1597 (Rfree = 0.000) for 10145 atoms. Found 36 (65 requested) and removed 38 (32 requested) atoms. Cycle 34: After refmac, R = 0.1558 (Rfree = 0.000) for 10124 atoms. Found 35 (65 requested) and removed 40 (32 requested) atoms. Cycle 35: After refmac, R = 0.1548 (Rfree = 0.000) for 10105 atoms. Found 50 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 10427 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 10440 seeds are put forward Round 1: 571 peptides, 106 chains. Longest chain 18 peptides. Score 0.351 Round 2: 664 peptides, 107 chains. Longest chain 36 peptides. Score 0.448 Round 3: 651 peptides, 105 chains. Longest chain 21 peptides. Score 0.443 Round 4: 653 peptides, 98 chains. Longest chain 26 peptides. Score 0.476 Round 5: 656 peptides, 94 chains. Longest chain 34 peptides. Score 0.497 Taking the results from Round 5 Chains 95, Residues 562, Estimated correctness of the model 0.0 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23396 restraints for refining 10182 atoms. 21059 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1761 (Rfree = 0.000) for 10182 atoms. Found 54 (65 requested) and removed 49 (32 requested) atoms. Cycle 37: After refmac, R = 0.1639 (Rfree = 0.000) for 10159 atoms. Found 36 (65 requested) and removed 40 (32 requested) atoms. Cycle 38: After refmac, R = 0.1586 (Rfree = 0.000) for 10145 atoms. Found 45 (65 requested) and removed 37 (32 requested) atoms. Cycle 39: After refmac, R = 0.1570 (Rfree = 0.000) for 10139 atoms. Found 41 (65 requested) and removed 35 (32 requested) atoms. Cycle 40: After refmac, R = 0.1556 (Rfree = 0.000) for 10141 atoms. Found 40 (65 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 10419 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 10454 seeds are put forward Round 1: 534 peptides, 103 chains. Longest chain 15 peptides. Score 0.323 Round 2: 597 peptides, 98 chains. Longest chain 18 peptides. Score 0.418 Round 3: 631 peptides, 100 chains. Longest chain 18 peptides. Score 0.445 Round 4: 640 peptides, 93 chains. Longest chain 25 peptides. Score 0.486 Round 5: 644 peptides, 95 chains. Longest chain 20 peptides. Score 0.481 Taking the results from Round 4 Chains 93, Residues 547, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 16761 reflections ( 98.94 % complete ) and 23741 restraints for refining 10182 atoms. 21594 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1690 (Rfree = 0.000) for 10182 atoms. Found 51 (65 requested) and removed 41 (32 requested) atoms. Cycle 42: After refmac, R = 0.1665 (Rfree = 0.000) for 10157 atoms. Found 52 (65 requested) and removed 36 (32 requested) atoms. Cycle 43: After refmac, R = 0.1610 (Rfree = 0.000) for 10158 atoms. Found 61 (65 requested) and removed 41 (32 requested) atoms. Cycle 44: After refmac, R = 0.1606 (Rfree = 0.000) for 10160 atoms. Found 64 (65 requested) and removed 38 (32 requested) atoms. Cycle 45: After refmac, R = 0.1522 (Rfree = 0.000) for 10174 atoms. Found 54 (65 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 10450 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 10475 seeds are put forward Round 1: 521 peptides, 99 chains. Longest chain 13 peptides. Score 0.327 Round 2: 598 peptides, 94 chains. Longest chain 19 peptides. Score 0.438 Round 3: 594 peptides, 90 chains. Longest chain 20 peptides. Score 0.452 Round 4: 575 peptides, 93 chains. Longest chain 17 peptides. Score 0.418 Round 5: 579 peptides, 88 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 92, Residues 504, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 92 chains (504 residues) following loop building 3 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16761 reflections ( 98.94 % complete ) and 23681 restraints for refining 10178 atoms. 21665 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1610 (Rfree = 0.000) for 10178 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1562 (Rfree = 0.000) for 10104 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1553 (Rfree = 0.000) for 10059 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1484 (Rfree = 0.000) for 10017 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:02:35 GMT 2018 Job finished. TimeTaking 154.63 Used memory is bytes: 25115872