Mon 24 Dec 00:44:33 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 1vrb-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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/1vrb-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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 00:44:38 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/1vrb-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.2-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 972 and 0 Target number of residues in the AU: 972 Target solvent content: 0.6290 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.2-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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: 48.979 3.200 Wilson plot Bfac: 66.01 23615 reflections ( 96.55 % complete ) and 0 restraints for refining 12045 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3294 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2780 (Rfree = 0.000) for 12045 atoms. Found 82 (108 requested) and removed 173 (54 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 12193 seeds are put forward NCS extension: 0 residues added, 12193 seeds are put forward Round 1: 525 peptides, 106 chains. Longest chain 12 peptides. Score 0.300 Round 2: 632 peptides, 101 chains. Longest chain 15 peptides. Score 0.449 Round 3: 675 peptides, 100 chains. Longest chain 26 peptides. Score 0.497 Round 4: 731 peptides, 105 chains. Longest chain 19 peptides. Score 0.531 Round 5: 739 peptides, 103 chains. Longest chain 21 peptides. Score 0.546 Taking the results from Round 5 Chains 108, Residues 636, Estimated correctness of the model 25.7 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22710 restraints for refining 9985 atoms. 20144 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2640 (Rfree = 0.000) for 9985 atoms. Found 80 (89 requested) and removed 74 (44 requested) atoms. Cycle 2: After refmac, R = 0.2500 (Rfree = 0.000) for 9887 atoms. Found 48 (89 requested) and removed 59 (44 requested) atoms. Cycle 3: After refmac, R = 0.2384 (Rfree = 0.000) for 9807 atoms. Found 38 (88 requested) and removed 56 (44 requested) atoms. Cycle 4: After refmac, R = 0.2302 (Rfree = 0.000) for 9754 atoms. Found 25 (87 requested) and removed 54 (43 requested) atoms. Cycle 5: After refmac, R = 0.2295 (Rfree = 0.000) for 9698 atoms. Found 29 (87 requested) and removed 51 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 9976 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 9987 seeds are put forward Round 1: 646 peptides, 109 chains. Longest chain 16 peptides. Score 0.426 Round 2: 723 peptides, 106 chains. Longest chain 24 peptides. Score 0.519 Round 3: 733 peptides, 103 chains. Longest chain 28 peptides. Score 0.541 Round 4: 744 peptides, 97 chains. Longest chain 30 peptides. Score 0.575 Round 5: 760 peptides, 101 chains. Longest chain 21 peptides. Score 0.573 Taking the results from Round 4 Chains 99, Residues 647, Estimated correctness of the model 34.1 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 21933 restraints for refining 9794 atoms. 19262 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2443 (Rfree = 0.000) for 9794 atoms. Found 58 (87 requested) and removed 89 (43 requested) atoms. Cycle 7: After refmac, R = 0.2333 (Rfree = 0.000) for 9728 atoms. Found 26 (87 requested) and removed 59 (43 requested) atoms. Cycle 8: After refmac, R = 0.2273 (Rfree = 0.000) for 9675 atoms. Found 27 (87 requested) and removed 57 (43 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2220 (Rfree = 0.000) for 9634 atoms. Found 21 (86 requested) and removed 54 (43 requested) atoms. Cycle 10: After refmac, R = 0.2190 (Rfree = 0.000) for 9588 atoms. Found 20 (86 requested) and removed 52 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 9864 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 9894 seeds are put forward Round 1: 700 peptides, 117 chains. Longest chain 17 peptides. Score 0.447 Round 2: 751 peptides, 102 chains. Longest chain 24 peptides. Score 0.561 Round 3: 745 peptides, 108 chains. Longest chain 27 peptides. Score 0.531 Round 4: 780 peptides, 110 chains. Longest chain 31 peptides. Score 0.555 Round 5: 763 peptides, 102 chains. Longest chain 21 peptides. Score 0.572 Taking the results from Round 5 Chains 109, Residues 661, Estimated correctness of the model 33.3 % 11 chains (117 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 21587 restraints for refining 9990 atoms. 18593 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 9990 atoms. Found 60 (89 requested) and removed 86 (44 requested) atoms. Cycle 12: After refmac, R = 0.2267 (Rfree = 0.000) for 9933 atoms. Found 21 (89 requested) and removed 51 (44 requested) atoms. Cycle 13: After refmac, R = 0.2216 (Rfree = 0.000) for 9881 atoms. Found 29 (88 requested) and removed 54 (44 requested) atoms. Cycle 14: After refmac, R = 0.2177 (Rfree = 0.000) for 9837 atoms. Found 19 (88 requested) and removed 45 (44 requested) atoms. Cycle 15: After refmac, R = 0.2120 (Rfree = 0.000) for 9796 atoms. Found 14 (88 requested) and removed 51 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 10057 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 10075 seeds are put forward Round 1: 607 peptides, 98 chains. Longest chain 14 peptides. Score 0.436 Round 2: 708 peptides, 105 chains. Longest chain 22 peptides. Score 0.508 Round 3: 729 peptides, 94 chains. Longest chain 27 peptides. Score 0.574 Round 4: 713 peptides, 97 chains. Longest chain 20 peptides. Score 0.547 Round 5: 725 peptides, 96 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 3 Chains 98, Residues 635, Estimated correctness of the model 33.9 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22381 restraints for refining 9991 atoms. 19834 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2341 (Rfree = 0.000) for 9991 atoms. Found 65 (89 requested) and removed 61 (44 requested) atoms. Cycle 17: After refmac, R = 0.2220 (Rfree = 0.000) for 9976 atoms. Found 20 (89 requested) and removed 50 (44 requested) atoms. Cycle 18: After refmac, R = 0.2156 (Rfree = 0.000) for 9940 atoms. Found 25 (89 requested) and removed 46 (44 requested) atoms. Cycle 19: After refmac, R = 0.2085 (Rfree = 0.000) for 9905 atoms. Found 11 (89 requested) and removed 44 (44 requested) atoms. Cycle 20: After refmac, R = 0.2068 (Rfree = 0.000) for 9865 atoms. Found 10 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 10125 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10140 seeds are put forward Round 1: 655 peptides, 111 chains. Longest chain 14 peptides. Score 0.427 Round 2: 723 peptides, 98 chains. Longest chain 28 peptides. Score 0.552 Round 3: 714 peptides, 105 chains. Longest chain 20 peptides. Score 0.514 Round 4: 727 peptides, 97 chains. Longest chain 21 peptides. Score 0.560 Round 5: 729 peptides, 102 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 4 Chains 97, Residues 630, Estimated correctness of the model 29.8 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22597 restraints for refining 9990 atoms. 20091 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 9990 atoms. Found 80 (89 requested) and removed 48 (44 requested) atoms. Cycle 22: After refmac, R = 0.2190 (Rfree = 0.000) for 10011 atoms. Found 30 (89 requested) and removed 44 (44 requested) atoms. Cycle 23: After refmac, R = 0.2096 (Rfree = 0.000) for 9983 atoms. Found 22 (89 requested) and removed 44 (44 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 9957 atoms. Found 16 (89 requested) and removed 44 (44 requested) atoms. Cycle 25: After refmac, R = 0.2065 (Rfree = 0.000) for 9925 atoms. Found 20 (89 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 10173 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 10184 seeds are put forward Round 1: 597 peptides, 99 chains. Longest chain 14 peptides. Score 0.420 Round 2: 656 peptides, 95 chains. Longest chain 24 peptides. Score 0.501 Round 3: 684 peptides, 99 chains. Longest chain 22 peptides. Score 0.511 Round 4: 672 peptides, 92 chains. Longest chain 21 peptides. Score 0.529 Round 5: 676 peptides, 91 chains. Longest chain 18 peptides. Score 0.537 Taking the results from Round 5 Chains 94, Residues 585, Estimated correctness of the model 23.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22683 restraints for refining 9990 atoms. 20314 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2193 (Rfree = 0.000) for 9990 atoms. Found 63 (89 requested) and removed 49 (44 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2065 (Rfree = 0.000) for 9983 atoms. Found 37 (89 requested) and removed 44 (44 requested) atoms. Cycle 28: After refmac, R = 0.2004 (Rfree = 0.000) for 9964 atoms. Found 26 (89 requested) and removed 44 (44 requested) atoms. Cycle 29: After refmac, R = 0.1964 (Rfree = 0.000) for 9929 atoms. Found 19 (89 requested) and removed 44 (44 requested) atoms. Cycle 30: After refmac, R = 0.1902 (Rfree = 0.000) for 9893 atoms. Found 21 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 10171 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 10183 seeds are put forward Round 1: 570 peptides, 109 chains. Longest chain 11 peptides. Score 0.339 Round 2: 656 peptides, 100 chains. Longest chain 19 peptides. Score 0.478 Round 3: 664 peptides, 98 chains. Longest chain 22 peptides. Score 0.495 Round 4: 652 peptides, 94 chains. Longest chain 18 peptides. Score 0.501 Round 5: 654 peptides, 92 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 5 Chains 92, Residues 562, Estimated correctness of the model 15.2 % 8 chains (51 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22652 restraints for refining 9991 atoms. 20313 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 9991 atoms. Found 68 (89 requested) and removed 57 (44 requested) atoms. Cycle 32: After refmac, R = 0.2060 (Rfree = 0.000) for 9986 atoms. Found 30 (89 requested) and removed 45 (44 requested) atoms. Cycle 33: After refmac, R = 0.2025 (Rfree = 0.000) for 9948 atoms. Found 19 (89 requested) and removed 45 (44 requested) atoms. Cycle 34: After refmac, R = 0.1990 (Rfree = 0.000) for 9908 atoms. Found 23 (89 requested) and removed 45 (44 requested) atoms. Cycle 35: After refmac, R = 0.1956 (Rfree = 0.000) for 9877 atoms. Found 19 (88 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 10113 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 10141 seeds are put forward Round 1: 549 peptides, 101 chains. Longest chain 17 peptides. Score 0.355 Round 2: 605 peptides, 98 chains. Longest chain 17 peptides. Score 0.433 Round 3: 625 peptides, 97 chains. Longest chain 18 peptides. Score 0.460 Round 4: 633 peptides, 96 chains. Longest chain 16 peptides. Score 0.473 Round 5: 635 peptides, 97 chains. Longest chain 17 peptides. Score 0.470 Taking the results from Round 4 Chains 99, Residues 537, Estimated correctness of the model 2.4 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22932 restraints for refining 9991 atoms. 20755 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2180 (Rfree = 0.000) for 9991 atoms. Found 65 (89 requested) and removed 57 (44 requested) atoms. Cycle 37: After refmac, R = 0.2036 (Rfree = 0.000) for 9980 atoms. Found 34 (89 requested) and removed 48 (44 requested) atoms. Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 9949 atoms. Found 29 (89 requested) and removed 47 (44 requested) atoms. Cycle 39: After refmac, R = 0.1967 (Rfree = 0.000) for 9918 atoms. Found 26 (89 requested) and removed 44 (44 requested) atoms. Cycle 40: After refmac, R = 0.1925 (Rfree = 0.000) for 9886 atoms. Found 15 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 10126 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 10148 seeds are put forward Round 1: 478 peptides, 91 chains. Longest chain 11 peptides. Score 0.321 Round 2: 564 peptides, 97 chains. Longest chain 15 peptides. Score 0.392 Round 3: 599 peptides, 97 chains. Longest chain 19 peptides. Score 0.432 Round 4: 578 peptides, 92 chains. Longest chain 20 peptides. Score 0.433 Round 5: 585 peptides, 92 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 5 Chains 93, Residues 493, Estimated correctness of the model 0.0 % 9 chains (53 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22882 restraints for refining 9991 atoms. 20822 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2154 (Rfree = 0.000) for 9991 atoms. Found 53 (89 requested) and removed 52 (44 requested) atoms. Cycle 42: After refmac, R = 0.2071 (Rfree = 0.000) for 9977 atoms. Found 35 (89 requested) and removed 50 (44 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 9945 atoms. Found 31 (89 requested) and removed 48 (44 requested) atoms. Cycle 44: After refmac, R = 0.2018 (Rfree = 0.000) for 9916 atoms. Found 26 (89 requested) and removed 45 (44 requested) atoms. Cycle 45: After refmac, R = 0.1945 (Rfree = 0.000) for 9891 atoms. Found 18 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 10124 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10141 seeds are put forward Round 1: 468 peptides, 90 chains. Longest chain 12 peptides. Score 0.313 Round 2: 519 peptides, 83 chains. Longest chain 21 peptides. Score 0.411 Round 3: 541 peptides, 88 chains. Longest chain 16 peptides. Score 0.411 Round 4: 524 peptides, 81 chains. Longest chain 14 peptides. Score 0.426 Round 5: 552 peptides, 88 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 81, Residues 443, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 81 chains (443 residues) following loop building 5 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23615 reflections ( 96.55 % complete ) and 23343 restraints for refining 9990 atoms. 21581 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2179 (Rfree = 0.000) for 9990 atoms. Found 0 (89 requested) and removed 44 (44 requested) atoms. Cycle 47: After refmac, R = 0.2095 (Rfree = 0.000) for 9928 atoms. Found 0 (89 requested) and removed 30 (44 requested) atoms. Cycle 48: After refmac, R = 0.2104 (Rfree = 0.000) for 9883 atoms. Found 0 (88 requested) and removed 36 (44 requested) atoms. Cycle 49: After refmac, R = 0.2116 (Rfree = 0.000) for 9840 atoms. TimeTaking 116.15