Mon 24 Dec 00:31:31 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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/2obn-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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 00:31:37 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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 948 and 0 Target number of residues in the AU: 948 Target solvent content: 0.6204 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-3.2-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.2-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 3.200 Wilson plot Bfac: 61.60 21957 reflections ( 99.70 % complete ) and 0 restraints for refining 12346 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2947 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2222 (Rfree = 0.000) for 12346 atoms. Found 56 (110 requested) and removed 102 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 12579 seeds are put forward NCS extension: 0 residues added, 12579 seeds are put forward Round 1: 659 peptides, 118 chains. Longest chain 12 peptides. Score 0.407 Round 2: 832 peptides, 118 chains. Longest chain 22 peptides. Score 0.584 Round 3: 876 peptides, 108 chains. Longest chain 37 peptides. Score 0.657 Round 4: 918 peptides, 109 chains. Longest chain 33 peptides. Score 0.684 Round 5: 909 peptides, 108 chains. Longest chain 26 peptides. Score 0.681 Taking the results from Round 4 Chains 116, Residues 809, Estimated correctness of the model 61.7 % 18 chains (160 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 20656 restraints for refining 10195 atoms. 17041 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2312 (Rfree = 0.000) for 10195 atoms. Found 67 (91 requested) and removed 75 (45 requested) atoms. Cycle 2: After refmac, R = 0.2132 (Rfree = 0.000) for 10050 atoms. Found 29 (91 requested) and removed 62 (45 requested) atoms. Cycle 3: After refmac, R = 0.2062 (Rfree = 0.000) for 9951 atoms. Found 24 (89 requested) and removed 50 (44 requested) atoms. Cycle 4: After refmac, R = 0.2037 (Rfree = 0.000) for 9902 atoms. Found 21 (89 requested) and removed 47 (44 requested) atoms. Cycle 5: After refmac, R = 0.1997 (Rfree = 0.000) for 9860 atoms. Found 13 (88 requested) and removed 47 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10129 seeds are put forward NCS extension: 24 residues added (13 deleted due to clashes), 10153 seeds are put forward Round 1: 802 peptides, 116 chains. Longest chain 21 peptides. Score 0.564 Round 2: 900 peptides, 103 chains. Longest chain 31 peptides. Score 0.691 Round 3: 886 peptides, 99 chains. Longest chain 39 peptides. Score 0.694 Round 4: 890 peptides, 98 chains. Longest chain 30 peptides. Score 0.700 Round 5: 900 peptides, 101 chains. Longest chain 44 peptides. Score 0.697 Taking the results from Round 4 Chains 109, Residues 792, Estimated correctness of the model 65.2 % 17 chains (190 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21183 restraints for refining 10194 atoms. 17499 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2231 (Rfree = 0.000) for 10194 atoms. Found 52 (91 requested) and removed 73 (45 requested) atoms. Cycle 7: After refmac, R = 0.2005 (Rfree = 0.000) for 10132 atoms. Found 35 (91 requested) and removed 53 (45 requested) atoms. Cycle 8: After refmac, R = 0.1896 (Rfree = 0.000) for 10089 atoms. Found 16 (90 requested) and removed 45 (45 requested) atoms. Cycle 9: After refmac, R = 0.1864 (Rfree = 0.000) for 10044 atoms. Found 18 (90 requested) and removed 45 (45 requested) atoms. Cycle 10: After refmac, R = 0.1875 (Rfree = 0.000) for 10003 atoms. Found 13 (89 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 10292 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 10308 seeds are put forward Round 1: 810 peptides, 115 chains. Longest chain 27 peptides. Score 0.576 Round 2: 879 peptides, 102 chains. Longest chain 32 peptides. Score 0.679 Round 3: 872 peptides, 100 chains. Longest chain 31 peptides. Score 0.681 Round 4: 878 peptides, 100 chains. Longest chain 37 peptides. Score 0.685 Round 5: 843 peptides, 94 chains. Longest chain 28 peptides. Score 0.680 Taking the results from Round 4 Chains 112, Residues 778, Estimated correctness of the model 61.9 % 22 chains (251 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 20447 restraints for refining 10193 atoms. 16621 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2204 (Rfree = 0.000) for 10193 atoms. Found 91 (91 requested) and removed 85 (45 requested) atoms. Cycle 12: After refmac, R = 0.1999 (Rfree = 0.000) for 10142 atoms. Found 35 (91 requested) and removed 55 (45 requested) atoms. Cycle 13: After refmac, R = 0.1919 (Rfree = 0.000) for 10103 atoms. Found 24 (90 requested) and removed 46 (45 requested) atoms. Cycle 14: After refmac, R = 0.1928 (Rfree = 0.000) for 10069 atoms. Found 26 (90 requested) and removed 45 (45 requested) atoms. Cycle 15: After refmac, R = 0.1848 (Rfree = 0.000) for 10040 atoms. Found 19 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10354 seeds are put forward NCS extension: 25 residues added (14 deleted due to clashes), 10379 seeds are put forward Round 1: 736 peptides, 107 chains. Longest chain 20 peptides. Score 0.539 Round 2: 818 peptides, 97 chains. Longest chain 28 peptides. Score 0.650 Round 3: 832 peptides, 97 chains. Longest chain 27 peptides. Score 0.661 Round 4: 868 peptides, 93 chains. Longest chain 26 peptides. Score 0.701 Round 5: 840 peptides, 93 chains. Longest chain 28 peptides. Score 0.681 Taking the results from Round 4 Chains 98, Residues 775, Estimated correctness of the model 65.4 % 14 chains (166 residues) have been docked in sequence Building loops using Loopy2018 98 chains (775 residues) following loop building 14 chains (166 residues) in sequence following loop building ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21126 restraints for refining 10195 atoms. 17560 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2081 (Rfree = 0.000) for 10195 atoms. Found 67 (91 requested) and removed 69 (45 requested) atoms. Cycle 17: After refmac, R = 0.1962 (Rfree = 0.000) for 10168 atoms. Found 23 (89 requested) and removed 48 (45 requested) atoms. Cycle 18: After refmac, R = 0.1915 (Rfree = 0.000) for 10126 atoms. Found 27 (87 requested) and removed 47 (45 requested) atoms. Cycle 19: After refmac, R = 0.1859 (Rfree = 0.000) for 10101 atoms. Found 32 (85 requested) and removed 45 (45 requested) atoms. Cycle 20: After refmac, R = 0.1765 (Rfree = 0.000) for 10076 atoms. Found 28 (83 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10392 seeds are put forward NCS extension: 24 residues added (13 deleted due to clashes), 10416 seeds are put forward Round 1: 718 peptides, 109 chains. Longest chain 18 peptides. Score 0.513 Round 2: 848 peptides, 104 chains. Longest chain 26 peptides. Score 0.649 Round 3: 842 peptides, 99 chains. Longest chain 22 peptides. Score 0.662 Round 4: 841 peptides, 107 chains. Longest chain 37 peptides. Score 0.633 Round 5: 848 peptides, 100 chains. Longest chain 27 peptides. Score 0.663 Taking the results from Round 5 Chains 109, Residues 748, Estimated correctness of the model 56.9 % 13 chains (111 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21502 restraints for refining 10196 atoms. 18253 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2056 (Rfree = 0.000) for 10196 atoms. Found 62 (82 requested) and removed 56 (45 requested) atoms. Cycle 22: After refmac, R = 0.1929 (Rfree = 0.000) for 10181 atoms. Found 38 (82 requested) and removed 48 (45 requested) atoms. Cycle 23: After refmac, R = 0.1853 (Rfree = 0.000) for 10150 atoms. Found 22 (82 requested) and removed 45 (45 requested) atoms. Cycle 24: After refmac, R = 0.1777 (Rfree = 0.000) for 10119 atoms. Found 22 (81 requested) and removed 45 (45 requested) atoms. Cycle 25: After refmac, R = 0.1756 (Rfree = 0.000) for 10087 atoms. Found 24 (81 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 10342 seeds are put forward NCS extension: 13 residues added (8 deleted due to clashes), 10355 seeds are put forward Round 1: 690 peptides, 110 chains. Longest chain 21 peptides. Score 0.479 Round 2: 739 peptides, 97 chains. Longest chain 37 peptides. Score 0.584 Round 3: 755 peptides, 96 chains. Longest chain 29 peptides. Score 0.602 Round 4: 767 peptides, 94 chains. Longest chain 32 peptides. Score 0.620 Round 5: 772 peptides, 96 chains. Longest chain 25 peptides. Score 0.617 Taking the results from Round 4 Chains 95, Residues 673, Estimated correctness of the model 46.3 % 8 chains (70 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22438 restraints for refining 10196 atoms. 19582 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2057 (Rfree = 0.000) for 10196 atoms. Found 73 (82 requested) and removed 54 (45 requested) atoms. Cycle 27: After refmac, R = 0.1840 (Rfree = 0.000) for 10195 atoms. Found 19 (82 requested) and removed 46 (45 requested) atoms. Cycle 28: After refmac, R = 0.1821 (Rfree = 0.000) for 10156 atoms. Found 19 (82 requested) and removed 45 (45 requested) atoms. Cycle 29: After refmac, R = 0.1745 (Rfree = 0.000) for 10127 atoms. Found 18 (81 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1720 (Rfree = 0.000) for 10093 atoms. Found 14 (81 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10352 seeds are put forward NCS extension: 25 residues added (8 deleted due to clashes), 10377 seeds are put forward Round 1: 662 peptides, 110 chains. Longest chain 18 peptides. Score 0.449 Round 2: 711 peptides, 88 chains. Longest chain 25 peptides. Score 0.595 Round 3: 744 peptides, 94 chains. Longest chain 25 peptides. Score 0.600 Round 4: 755 peptides, 90 chains. Longest chain 37 peptides. Score 0.625 Round 5: 765 peptides, 95 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 4 Chains 96, Residues 665, Estimated correctness of the model 47.6 % 8 chains (71 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22592 restraints for refining 10196 atoms. 19811 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2010 (Rfree = 0.000) for 10196 atoms. Found 73 (82 requested) and removed 57 (45 requested) atoms. Cycle 32: After refmac, R = 0.1820 (Rfree = 0.000) for 10199 atoms. Found 30 (82 requested) and removed 45 (45 requested) atoms. Cycle 33: After refmac, R = 0.1792 (Rfree = 0.000) for 10173 atoms. Found 22 (82 requested) and removed 46 (45 requested) atoms. Cycle 34: After refmac, R = 0.1726 (Rfree = 0.000) for 10149 atoms. Found 13 (82 requested) and removed 46 (45 requested) atoms. Cycle 35: After refmac, R = 0.1716 (Rfree = 0.000) for 10109 atoms. Found 22 (81 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10345 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 10367 seeds are put forward Round 1: 646 peptides, 106 chains. Longest chain 18 peptides. Score 0.450 Round 2: 706 peptides, 99 chains. Longest chain 36 peptides. Score 0.544 Round 3: 696 peptides, 95 chains. Longest chain 23 peptides. Score 0.552 Round 4: 692 peptides, 94 chains. Longest chain 29 peptides. Score 0.552 Round 5: 706 peptides, 98 chains. Longest chain 25 peptides. Score 0.549 Taking the results from Round 4 Chains 99, Residues 598, Estimated correctness of the model 27.5 % 8 chains (66 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22953 restraints for refining 10195 atoms. 20426 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1925 (Rfree = 0.000) for 10195 atoms. Found 68 (82 requested) and removed 54 (45 requested) atoms. Cycle 37: After refmac, R = 0.1804 (Rfree = 0.000) for 10194 atoms. Found 27 (82 requested) and removed 46 (45 requested) atoms. Cycle 38: After refmac, R = 0.1766 (Rfree = 0.000) for 10166 atoms. Found 37 (82 requested) and removed 45 (45 requested) atoms. Cycle 39: After refmac, R = 0.1722 (Rfree = 0.000) for 10153 atoms. Found 29 (82 requested) and removed 47 (45 requested) atoms. Cycle 40: After refmac, R = 0.1700 (Rfree = 0.000) for 10128 atoms. Found 30 (81 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 10399 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 10417 seeds are put forward Round 1: 603 peptides, 108 chains. Longest chain 13 peptides. Score 0.391 Round 2: 681 peptides, 102 chains. Longest chain 27 peptides. Score 0.506 Round 3: 722 peptides, 107 chains. Longest chain 27 peptides. Score 0.525 Round 4: 692 peptides, 93 chains. Longest chain 28 peptides. Score 0.557 Round 5: 683 peptides, 97 chains. Longest chain 25 peptides. Score 0.530 Taking the results from Round 4 Chains 97, Residues 599, Estimated correctness of the model 28.9 % 11 chains (93 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22586 restraints for refining 10196 atoms. 20007 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1850 (Rfree = 0.000) for 10196 atoms. Found 53 (82 requested) and removed 56 (45 requested) atoms. Cycle 42: After refmac, R = 0.1733 (Rfree = 0.000) for 10172 atoms. Found 16 (82 requested) and removed 48 (45 requested) atoms. Cycle 43: After refmac, R = 0.1715 (Rfree = 0.000) for 10133 atoms. Found 22 (82 requested) and removed 45 (45 requested) atoms. Cycle 44: After refmac, R = 0.1703 (Rfree = 0.000) for 10105 atoms. Found 27 (81 requested) and removed 45 (45 requested) atoms. Cycle 45: After refmac, R = 0.1656 (Rfree = 0.000) for 10083 atoms. Found 14 (81 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10323 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 10334 seeds are put forward Round 1: 557 peptides, 101 chains. Longest chain 16 peptides. Score 0.372 Round 2: 632 peptides, 95 chains. Longest chain 17 peptides. Score 0.487 Round 3: 617 peptides, 93 chains. Longest chain 16 peptides. Score 0.480 Round 4: 621 peptides, 89 chains. Longest chain 26 peptides. Score 0.503 Round 5: 609 peptides, 87 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 94, Residues 532, Estimated correctness of the model 12.3 % 12 chains (75 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 94 chains (532 residues) following loop building 12 chains (75 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21957 reflections ( 99.70 % complete ) and 23293 restraints for refining 10196 atoms. 21018 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1784 (Rfree = 0.000) for 10196 atoms. Found 0 (82 requested) and removed 18 (45 requested) atoms. Cycle 47: After refmac, R = 0.1747 (Rfree = 0.000) for 10166 atoms. Found 0 (82 requested) and removed 9 (45 requested) atoms. Cycle 48: After refmac, R = 0.1746 (Rfree = 0.000) for 10149 atoms. Found 0 (82 requested) and removed 2 (45 requested) atoms. Cycle 49: After refmac, R = 0.1681 (Rfree = 0.000) for 10143 atoms. Found 0 (82 requested) and removed 15 (45 requested) atoms. Writing output files ... TimeTaking 122.13