Sun 23 Dec 22:22:52 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 2obn-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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/2obn-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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 ============================================================ Sun 23 Dec 22:23:02 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/2obn-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-3.4-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 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-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.4-parrot-hancs.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 12347 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.2990 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2607 (Rfree = 0.000) for 12347 atoms. Found 82 (93 requested) and removed 92 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 12594 seeds are put forward NCS extension: 0 residues added, 12594 seeds are put forward Round 1: 569 peptides, 110 chains. Longest chain 15 peptides. Score 0.339 Round 2: 711 peptides, 108 chains. Longest chain 14 peptides. Score 0.510 Round 3: 764 peptides, 106 chains. Longest chain 26 peptides. Score 0.570 Round 4: 780 peptides, 109 chains. Longest chain 25 peptides. Score 0.573 Round 5: 806 peptides, 106 chains. Longest chain 28 peptides. Score 0.607 Taking the results from Round 5 Chains 116, Residues 700, Estimated correctness of the model 30.9 % 11 chains (91 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22526 restraints for refining 10152 atoms. 19566 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2267 (Rfree = 0.000) for 10152 atoms. Found 55 (76 requested) and removed 58 (38 requested) atoms. Cycle 2: After refmac, R = 0.2061 (Rfree = 0.000) for 10021 atoms. Found 31 (76 requested) and removed 52 (38 requested) atoms. Cycle 3: After refmac, R = 0.1959 (Rfree = 0.000) for 9942 atoms. Found 20 (75 requested) and removed 49 (37 requested) atoms. Cycle 4: After refmac, R = 0.1885 (Rfree = 0.000) for 9895 atoms. Found 11 (74 requested) and removed 41 (37 requested) atoms. Cycle 5: After refmac, R = 0.1886 (Rfree = 0.000) for 9843 atoms. Found 21 (74 requested) and removed 43 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10185 seeds are put forward NCS extension: 46 residues added (2 deleted due to clashes), 10231 seeds are put forward Round 1: 696 peptides, 122 chains. Longest chain 16 peptides. Score 0.429 Round 2: 767 peptides, 113 chains. Longest chain 25 peptides. Score 0.544 Round 3: 782 peptides, 108 chains. Longest chain 22 peptides. Score 0.578 Round 4: 774 peptides, 101 chains. Longest chain 30 peptides. Score 0.599 Round 5: 801 peptides, 104 chains. Longest chain 21 peptides. Score 0.611 Taking the results from Round 5 Chains 113, Residues 697, Estimated correctness of the model 32.2 % 15 chains (119 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22481 restraints for refining 10152 atoms. 19425 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2142 (Rfree = 0.000) for 10152 atoms. Found 42 (76 requested) and removed 65 (38 requested) atoms. Cycle 7: After refmac, R = 0.1960 (Rfree = 0.000) for 10060 atoms. Found 32 (76 requested) and removed 52 (38 requested) atoms. Cycle 8: After refmac, R = 0.1856 (Rfree = 0.000) for 10005 atoms. Found 13 (75 requested) and removed 45 (37 requested) atoms. Cycle 9: After refmac, R = 0.1791 (Rfree = 0.000) for 9956 atoms. Found 15 (75 requested) and removed 44 (37 requested) atoms. Cycle 10: After refmac, R = 0.1743 (Rfree = 0.000) for 9902 atoms. Found 18 (74 requested) and removed 42 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10244 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 10256 seeds are put forward Round 1: 659 peptides, 108 chains. Longest chain 17 peptides. Score 0.455 Round 2: 741 peptides, 101 chains. Longest chain 18 peptides. Score 0.569 Round 3: 758 peptides, 105 chains. Longest chain 18 peptides. Score 0.569 Round 4: 800 peptides, 102 chains. Longest chain 27 peptides. Score 0.617 Round 5: 793 peptides, 106 chains. Longest chain 23 peptides. Score 0.596 Taking the results from Round 4 Chains 113, Residues 698, Estimated correctness of the model 34.1 % 15 chains (125 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22091 restraints for refining 10154 atoms. 19048 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2009 (Rfree = 0.000) for 10154 atoms. Found 45 (76 requested) and removed 72 (38 requested) atoms. Cycle 12: After refmac, R = 0.1862 (Rfree = 0.000) for 10087 atoms. Found 17 (76 requested) and removed 52 (38 requested) atoms. Cycle 13: After refmac, R = 0.1786 (Rfree = 0.000) for 10034 atoms. Found 16 (75 requested) and removed 40 (37 requested) atoms. Cycle 14: After refmac, R = 0.1731 (Rfree = 0.000) for 9998 atoms. Found 18 (75 requested) and removed 47 (37 requested) atoms. Cycle 15: After refmac, R = 0.1686 (Rfree = 0.000) for 9954 atoms. Found 11 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10234 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 10249 seeds are put forward Round 1: 673 peptides, 115 chains. Longest chain 20 peptides. Score 0.437 Round 2: 781 peptides, 105 chains. Longest chain 36 peptides. Score 0.589 Round 3: 771 peptides, 110 chains. Longest chain 24 peptides. Score 0.560 Round 4: 795 peptides, 101 chains. Longest chain 32 peptides. Score 0.617 Round 5: 789 peptides, 104 chains. Longest chain 28 peptides. Score 0.600 Taking the results from Round 4 Chains 104, Residues 694, Estimated correctness of the model 34.1 % 13 chains (126 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 21994 restraints for refining 10151 atoms. 18902 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1942 (Rfree = 0.000) for 10151 atoms. Found 42 (76 requested) and removed 73 (38 requested) atoms. Cycle 17: After refmac, R = 0.1793 (Rfree = 0.000) for 10076 atoms. Found 25 (76 requested) and removed 40 (38 requested) atoms. Cycle 18: After refmac, R = 0.1732 (Rfree = 0.000) for 10049 atoms. Found 23 (75 requested) and removed 42 (37 requested) atoms. Cycle 19: After refmac, R = 0.1693 (Rfree = 0.000) for 10014 atoms. Found 20 (75 requested) and removed 39 (37 requested) atoms. Cycle 20: After refmac, R = 0.1597 (Rfree = 0.000) for 9982 atoms. Found 19 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10299 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 10326 seeds are put forward Round 1: 643 peptides, 109 chains. Longest chain 19 peptides. Score 0.432 Round 2: 734 peptides, 103 chains. Longest chain 27 peptides. Score 0.554 Round 3: 727 peptides, 101 chains. Longest chain 21 peptides. Score 0.556 Round 4: 710 peptides, 95 chains. Longest chain 24 peptides. Score 0.565 Round 5: 725 peptides, 99 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 4 Chains 99, Residues 615, Estimated correctness of the model 16.8 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22964 restraints for refining 10154 atoms. 20409 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1847 (Rfree = 0.000) for 10154 atoms. Found 55 (76 requested) and removed 47 (38 requested) atoms. Cycle 22: After refmac, R = 0.1728 (Rfree = 0.000) for 10128 atoms. Found 20 (76 requested) and removed 41 (38 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1643 (Rfree = 0.000) for 10082 atoms. Found 26 (76 requested) and removed 42 (38 requested) atoms. Cycle 24: After refmac, R = 0.1604 (Rfree = 0.000) for 10047 atoms. Found 28 (76 requested) and removed 42 (38 requested) atoms. Cycle 25: After refmac, R = 0.1559 (Rfree = 0.000) for 10018 atoms. Found 30 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10308 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 10340 seeds are put forward Round 1: 586 peptides, 105 chains. Longest chain 15 peptides. Score 0.386 Round 2: 663 peptides, 97 chains. Longest chain 21 peptides. Score 0.510 Round 3: 674 peptides, 96 chains. Longest chain 23 peptides. Score 0.526 Round 4: 716 peptides, 100 chains. Longest chain 21 peptides. Score 0.550 Round 5: 698 peptides, 99 chains. Longest chain 28 peptides. Score 0.537 Taking the results from Round 4 Chains 104, Residues 616, Estimated correctness of the model 11.5 % 11 chains (76 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22898 restraints for refining 10154 atoms. 20305 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1874 (Rfree = 0.000) for 10154 atoms. Found 48 (76 requested) and removed 56 (38 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1772 (Rfree = 0.000) for 10097 atoms. Found 39 (76 requested) and removed 39 (38 requested) atoms. Cycle 28: After refmac, R = 0.1674 (Rfree = 0.000) for 10066 atoms. Found 29 (76 requested) and removed 39 (38 requested) atoms. Cycle 29: After refmac, R = 0.1640 (Rfree = 0.000) for 10033 atoms. Found 35 (75 requested) and removed 43 (37 requested) atoms. Cycle 30: After refmac, R = 0.1572 (Rfree = 0.000) for 10012 atoms. Found 25 (75 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10268 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 10292 seeds are put forward Round 1: 568 peptides, 105 chains. Longest chain 21 peptides. Score 0.364 Round 2: 649 peptides, 106 chains. Longest chain 16 peptides. Score 0.453 Round 3: 673 peptides, 97 chains. Longest chain 21 peptides. Score 0.520 Round 4: 652 peptides, 95 chains. Longest chain 26 peptides. Score 0.508 Round 5: 658 peptides, 89 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 5 Chains 91, Residues 569, Estimated correctness of the model 8.3 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23187 restraints for refining 10153 atoms. 20820 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1862 (Rfree = 0.000) for 10153 atoms. Found 54 (76 requested) and removed 52 (38 requested) atoms. Cycle 32: After refmac, R = 0.1726 (Rfree = 0.000) for 10132 atoms. Found 31 (76 requested) and removed 44 (38 requested) atoms. Cycle 33: After refmac, R = 0.1648 (Rfree = 0.000) for 10108 atoms. Found 27 (76 requested) and removed 41 (38 requested) atoms. Cycle 34: After refmac, R = 0.1640 (Rfree = 0.000) for 10074 atoms. Found 24 (76 requested) and removed 41 (38 requested) atoms. Cycle 35: After refmac, R = 0.1594 (Rfree = 0.000) for 10049 atoms. Found 27 (75 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10306 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 10319 seeds are put forward Round 1: 552 peptides, 102 chains. Longest chain 13 peptides. Score 0.360 Round 2: 594 peptides, 93 chains. Longest chain 14 peptides. Score 0.455 Round 3: 610 peptides, 93 chains. Longest chain 16 peptides. Score 0.473 Round 4: 599 peptides, 92 chains. Longest chain 16 peptides. Score 0.465 Round 5: 619 peptides, 95 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 5 Chains 95, Residues 524, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23617 restraints for refining 10153 atoms. 21529 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1722 (Rfree = 0.000) for 10153 atoms. Found 45 (76 requested) and removed 44 (38 requested) atoms. Cycle 37: After refmac, R = 0.1615 (Rfree = 0.000) for 10124 atoms. Found 18 (76 requested) and removed 45 (38 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1604 (Rfree = 0.000) for 10083 atoms. Found 30 (76 requested) and removed 43 (38 requested) atoms. Cycle 39: After refmac, R = 0.1546 (Rfree = 0.000) for 10060 atoms. Found 23 (76 requested) and removed 40 (38 requested) atoms. Cycle 40: After refmac, R = 0.1352 (Rfree = 0.000) for 10037 atoms. Found 11 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10279 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 10296 seeds are put forward Round 1: 488 peptides, 92 chains. Longest chain 15 peptides. Score 0.333 Round 2: 551 peptides, 88 chains. Longest chain 17 peptides. Score 0.431 Round 3: 537 peptides, 82 chains. Longest chain 16 peptides. Score 0.445 Round 4: 565 peptides, 85 chains. Longest chain 20 peptides. Score 0.462 Round 5: 542 peptides, 82 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 4 Chains 89, Residues 480, Estimated correctness of the model 0.0 % 11 chains (68 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23349 restraints for refining 10154 atoms. 21304 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1635 (Rfree = 0.000) for 10154 atoms. Found 46 (76 requested) and removed 43 (38 requested) atoms. Cycle 42: After refmac, R = 0.1572 (Rfree = 0.000) for 10135 atoms. Found 31 (76 requested) and removed 43 (38 requested) atoms. Cycle 43: After refmac, R = 0.1598 (Rfree = 0.000) for 10120 atoms. Found 27 (76 requested) and removed 40 (38 requested) atoms. Cycle 44: After refmac, R = 0.1523 (Rfree = 0.000) for 10098 atoms. Found 34 (76 requested) and removed 42 (38 requested) atoms. Cycle 45: After refmac, R = 0.1512 (Rfree = 0.000) for 10084 atoms. Found 21 (76 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10312 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 10337 seeds are put forward Round 1: 499 peptides, 98 chains. Longest chain 19 peptides. Score 0.315 Round 2: 542 peptides, 94 chains. Longest chain 18 peptides. Score 0.390 Round 3: 544 peptides, 90 chains. Longest chain 21 peptides. Score 0.413 Round 4: 558 peptides, 93 chains. Longest chain 20 peptides. Score 0.414 Round 5: 558 peptides, 93 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 94, Residues 465, Estimated correctness of the model 0.0 % 9 chains (35 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 200 B and 212 B 92 chains (473 residues) following loop building 8 chains (46 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18320 reflections ( 99.66 % complete ) and 23717 restraints for refining 10154 atoms. 21807 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1623 (Rfree = 0.000) for 10154 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1596 (Rfree = 0.000) for 10088 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.1572 (Rfree = 0.000) for 10039 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Cycle 49: After refmac, R = 0.1523 (Rfree = 0.000) for 9993 atoms. TimeTaking 111.73