Mon 24 Dec 00:55:05 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 2obn-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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/2obn-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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 00:56:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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 907 and 0 Target number of residues in the AU: 907 Target solvent content: 0.6368 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-3.4-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11168 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: 73.214 3.400 Wilson plot Bfac: 70.07 18320 reflections ( 99.66 % complete ) and 0 restraints for refining 12440 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.2999 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2421 (Rfree = 0.000) for 12440 atoms. Found 74 (93 requested) and removed 90 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 12669 seeds are put forward NCS extension: 0 residues added, 12669 seeds are put forward Round 1: 612 peptides, 112 chains. Longest chain 11 peptides. Score 0.381 Round 2: 747 peptides, 113 chains. Longest chain 16 peptides. Score 0.524 Round 3: 805 peptides, 109 chains. Longest chain 20 peptides. Score 0.595 Round 4: 800 peptides, 111 chains. Longest chain 26 peptides. Score 0.583 Round 5: 825 peptides, 100 chains. Longest chain 42 peptides. Score 0.645 Taking the results from Round 5 Chains 110, Residues 725, Estimated correctness of the model 42.7 % 18 chains (158 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 21267 restraints for refining 10147 atoms. 17978 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2317 (Rfree = 0.000) for 10147 atoms. Found 64 (76 requested) and removed 65 (38 requested) atoms. Cycle 2: After refmac, R = 0.2063 (Rfree = 0.000) for 10045 atoms. Found 17 (76 requested) and removed 51 (38 requested) atoms. Cycle 3: After refmac, R = 0.2026 (Rfree = 0.000) for 9953 atoms. Found 18 (75 requested) and removed 45 (37 requested) atoms. Cycle 4: After refmac, R = 0.1931 (Rfree = 0.000) for 9895 atoms. Found 18 (74 requested) and removed 43 (37 requested) atoms. Cycle 5: After refmac, R = 0.1873 (Rfree = 0.000) for 9837 atoms. Found 17 (74 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 10151 seeds are put forward NCS extension: 20 residues added (12 deleted due to clashes), 10171 seeds are put forward Round 1: 697 peptides, 114 chains. Longest chain 29 peptides. Score 0.468 Round 2: 796 peptides, 110 chains. Longest chain 36 peptides. Score 0.583 Round 3: 816 peptides, 97 chains. Longest chain 26 peptides. Score 0.649 Round 4: 828 peptides, 102 chains. Longest chain 25 peptides. Score 0.640 Round 5: 860 peptides, 99 chains. Longest chain 23 peptides. Score 0.675 Taking the results from Round 5 Chains 104, Residues 761, Estimated correctness of the model 51.2 % 15 chains (153 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 21559 restraints for refining 10154 atoms. 18137 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2172 (Rfree = 0.000) for 10154 atoms. Found 59 (76 requested) and removed 77 (38 requested) atoms. Cycle 7: After refmac, R = 0.1988 (Rfree = 0.000) for 10081 atoms. Found 30 (76 requested) and removed 49 (38 requested) atoms. Cycle 8: After refmac, R = 0.1867 (Rfree = 0.000) for 10024 atoms. Found 24 (75 requested) and removed 52 (37 requested) atoms. Cycle 9: After refmac, R = 0.1782 (Rfree = 0.000) for 9961 atoms. Found 22 (75 requested) and removed 49 (37 requested) atoms. Cycle 10: After refmac, R = 0.1726 (Rfree = 0.000) for 9908 atoms. Found 19 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10196 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 10217 seeds are put forward Round 1: 713 peptides, 117 chains. Longest chain 17 peptides. Score 0.471 Round 2: 785 peptides, 102 chains. Longest chain 33 peptides. Score 0.605 Round 3: 816 peptides, 106 chains. Longest chain 21 peptides. Score 0.616 Round 4: 793 peptides, 101 chains. Longest chain 23 peptides. Score 0.615 Round 5: 809 peptides, 99 chains. Longest chain 40 peptides. Score 0.636 Taking the results from Round 5 Chains 105, Residues 710, Estimated correctness of the model 40.0 % 14 chains (129 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22190 restraints for refining 10153 atoms. 19023 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2129 (Rfree = 0.000) for 10153 atoms. Found 63 (76 requested) and removed 74 (38 requested) atoms. Cycle 12: After refmac, R = 0.1919 (Rfree = 0.000) for 10104 atoms. Found 26 (76 requested) and removed 52 (38 requested) atoms. Cycle 13: After refmac, R = 0.1808 (Rfree = 0.000) for 10057 atoms. Found 18 (76 requested) and removed 41 (38 requested) atoms. Cycle 14: After refmac, R = 0.1699 (Rfree = 0.000) for 10019 atoms. Found 15 (75 requested) and removed 38 (37 requested) atoms. Cycle 15: After refmac, R = 0.1639 (Rfree = 0.000) for 9983 atoms. Found 19 (75 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10329 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 10360 seeds are put forward Round 1: 658 peptides, 111 chains. Longest chain 14 peptides. Score 0.439 Round 2: 755 peptides, 112 chains. Longest chain 21 peptides. Score 0.536 Round 3: 784 peptides, 115 chains. Longest chain 15 peptides. Score 0.552 Round 4: 780 peptides, 114 chains. Longest chain 24 peptides. Score 0.552 Round 5: 754 peptides, 100 chains. Longest chain 30 peptides. Score 0.585 Taking the results from Round 5 Chains 105, Residues 654, Estimated correctness of the model 23.7 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22831 restraints for refining 10152 atoms. 20108 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1887 (Rfree = 0.000) for 10152 atoms. Found 59 (76 requested) and removed 52 (38 requested) atoms. Cycle 17: After refmac, R = 0.1677 (Rfree = 0.000) for 10128 atoms. Found 18 (76 requested) and removed 44 (38 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1636 (Rfree = 0.000) for 10080 atoms. Found 23 (76 requested) and removed 43 (38 requested) atoms. Cycle 19: After refmac, R = 0.1595 (Rfree = 0.000) for 10051 atoms. Found 12 (75 requested) and removed 37 (37 requested) atoms. Cycle 20: After refmac, R = 0.1549 (Rfree = 0.000) for 10015 atoms. Found 11 (75 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10334 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 10351 seeds are put forward Round 1: 648 peptides, 116 chains. Longest chain 16 peptides. Score 0.404 Round 2: 723 peptides, 103 chains. Longest chain 24 peptides. Score 0.544 Round 3: 716 peptides, 100 chains. Longest chain 24 peptides. Score 0.550 Round 4: 708 peptides, 107 chains. Longest chain 18 peptides. Score 0.511 Round 5: 713 peptides, 100 chains. Longest chain 22 peptides. Score 0.547 Taking the results from Round 3 Chains 107, Residues 616, Estimated correctness of the model 11.5 % 11 chains (89 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22926 restraints for refining 10153 atoms. 20293 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1862 (Rfree = 0.000) for 10153 atoms. Found 47 (76 requested) and removed 50 (38 requested) atoms. Cycle 22: After refmac, R = 0.1736 (Rfree = 0.000) for 10128 atoms. Found 26 (76 requested) and removed 40 (38 requested) atoms. Cycle 23: After refmac, R = 0.1651 (Rfree = 0.000) for 10095 atoms. Found 23 (76 requested) and removed 43 (38 requested) atoms. Cycle 24: After refmac, R = 0.1588 (Rfree = 0.000) for 10064 atoms. Found 25 (76 requested) and removed 40 (38 requested) atoms. Cycle 25: After refmac, R = 0.1542 (Rfree = 0.000) for 10042 atoms. Found 20 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10340 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 10356 seeds are put forward Round 1: 625 peptides, 112 chains. Longest chain 15 peptides. Score 0.397 Round 2: 688 peptides, 111 chains. Longest chain 18 peptides. Score 0.472 Round 3: 697 peptides, 103 chains. Longest chain 18 peptides. Score 0.518 Round 4: 718 peptides, 100 chains. Longest chain 18 peptides. Score 0.552 Round 5: 716 peptides, 108 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 4 Chains 108, Residues 618, Estimated correctness of the model 12.2 % 14 chains (93 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22907 restraints for refining 10154 atoms. 20292 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1828 (Rfree = 0.000) for 10154 atoms. Found 53 (76 requested) and removed 47 (38 requested) atoms. Cycle 27: After refmac, R = 0.1674 (Rfree = 0.000) for 10133 atoms. Found 20 (76 requested) and removed 42 (38 requested) atoms. Cycle 28: After refmac, R = 0.1639 (Rfree = 0.000) for 10096 atoms. Found 26 (76 requested) and removed 39 (38 requested) atoms. Cycle 29: After refmac, R = 0.1574 (Rfree = 0.000) for 10065 atoms. Found 27 (76 requested) and removed 42 (38 requested) atoms. Cycle 30: After refmac, R = 0.1516 (Rfree = 0.000) for 10039 atoms. Found 20 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10340 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10354 seeds are put forward Round 1: 594 peptides, 111 chains. Longest chain 15 peptides. Score 0.365 Round 2: 635 peptides, 100 chains. Longest chain 17 peptides. Score 0.467 Round 3: 674 peptides, 102 chains. Longest chain 23 peptides. Score 0.499 Round 4: 659 peptides, 103 chains. Longest chain 25 peptides. Score 0.478 Round 5: 683 peptides, 99 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 5 Chains 103, Residues 584, Estimated correctness of the model 1.2 % 12 chains (82 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23052 restraints for refining 10154 atoms. 20601 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1785 (Rfree = 0.000) for 10154 atoms. Found 55 (76 requested) and removed 46 (38 requested) atoms. Cycle 32: After refmac, R = 0.1619 (Rfree = 0.000) for 10137 atoms. Found 20 (76 requested) and removed 42 (38 requested) atoms. Cycle 33: After refmac, R = 0.1611 (Rfree = 0.000) for 10103 atoms. Found 29 (76 requested) and removed 38 (38 requested) atoms. Cycle 34: After refmac, R = 0.1567 (Rfree = 0.000) for 10086 atoms. Found 27 (76 requested) and removed 38 (38 requested) atoms. Cycle 35: After refmac, R = 0.1463 (Rfree = 0.000) for 10066 atoms. Found 16 (76 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10344 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 10362 seeds are put forward Round 1: 565 peptides, 105 chains. Longest chain 15 peptides. Score 0.361 Round 2: 631 peptides, 96 chains. Longest chain 18 peptides. Score 0.481 Round 3: 642 peptides, 103 chains. Longest chain 20 peptides. Score 0.460 Round 4: 666 peptides, 95 chains. Longest chain 18 peptides. Score 0.522 Round 5: 641 peptides, 97 chains. Longest chain 20 peptides. Score 0.487 Taking the results from Round 4 Chains 95, Residues 571, Estimated correctness of the model 1.2 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23338 restraints for refining 10152 atoms. 21000 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1646 (Rfree = 0.000) for 10152 atoms. Found 53 (76 requested) and removed 53 (38 requested) atoms. Cycle 37: After refmac, R = 0.1532 (Rfree = 0.000) for 10139 atoms. Found 13 (76 requested) and removed 40 (38 requested) atoms. Cycle 38: After refmac, R = 0.1521 (Rfree = 0.000) for 10102 atoms. Found 14 (76 requested) and removed 38 (38 requested) atoms. Cycle 39: After refmac, R = 0.1471 (Rfree = 0.000) for 10073 atoms. Found 14 (76 requested) and removed 38 (38 requested) atoms. Cycle 40: After refmac, R = 0.1465 (Rfree = 0.000) for 10046 atoms. Found 20 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10326 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10345 seeds are put forward Round 1: 536 peptides, 106 chains. Longest chain 11 peptides. Score 0.319 Round 2: 587 peptides, 99 chains. Longest chain 21 peptides. Score 0.417 Round 3: 603 peptides, 101 chains. Longest chain 18 peptides. Score 0.426 Round 4: 589 peptides, 94 chains. Longest chain 18 peptides. Score 0.445 Round 5: 597 peptides, 96 chains. Longest chain 20 peptides. Score 0.444 Taking the results from Round 4 Chains 96, Residues 495, Estimated correctness of the model 0.0 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23739 restraints for refining 10153 atoms. 21731 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1621 (Rfree = 0.000) for 10153 atoms. Found 34 (76 requested) and removed 44 (38 requested) atoms. Cycle 42: After refmac, R = 0.1551 (Rfree = 0.000) for 10120 atoms. Found 28 (76 requested) and removed 39 (38 requested) atoms. Cycle 43: After refmac, R = 0.1528 (Rfree = 0.000) for 10095 atoms. Found 24 (76 requested) and removed 39 (38 requested) atoms. Cycle 44: After refmac, R = 0.1499 (Rfree = 0.000) for 10065 atoms. Found 26 (76 requested) and removed 39 (38 requested) atoms. Cycle 45: After refmac, R = 0.1453 (Rfree = 0.000) for 10041 atoms. Found 37 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10369 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 10389 seeds are put forward Round 1: 453 peptides, 88 chains. Longest chain 12 peptides. Score 0.310 Round 2: 536 peptides, 87 chains. Longest chain 16 peptides. Score 0.419 Round 3: 547 peptides, 89 chains. Longest chain 18 peptides. Score 0.421 Round 4: 538 peptides, 87 chains. Longest chain 19 peptides. Score 0.421 Round 5: 559 peptides, 88 chains. Longest chain 22 peptides. Score 0.440 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 471, Estimated correctness of the model 0.0 % 13 chains (85 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (471 residues) following loop building 13 chains (85 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18320 reflections ( 99.66 % complete ) and 23415 restraints for refining 10153 atoms. 21355 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1610 (Rfree = 0.000) for 10153 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1546 (Rfree = 0.000) for 10091 atoms. Found 0 (76 requested) and removed 28 (38 requested) atoms. Cycle 48: After refmac, R = 0.1532 (Rfree = 0.000) for 10050 atoms. Found 0 (75 requested) and removed 16 (37 requested) atoms. Cycle 49: After refmac, R = 0.1501 (Rfree = 0.000) for 10028 atoms. Found 0 (75 requested) and removed 19 (37 requested) atoms. Writing output files ... TimeTaking 217.4