Mon 24 Dec 07:29:16 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkm-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-noncs ############### 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 07:29:20 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.6-parrot-noncs/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 1181 and 0 Target number of residues in the AU: 1181 Target solvent content: 0.6199 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.6-parrot-noncs.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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 14256 target number of atoms Had to go as low as 0.55 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: 75.160 3.600 Wilson plot Bfac: 61.41 20157 reflections ( 99.97 % complete ) and 0 restraints for refining 15791 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3156 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3059 (Rfree = 0.000) for 15791 atoms. Found 76 (101 requested) and removed 121 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 16065 seeds are put forward NCS extension: 0 residues added, 16065 seeds are put forward Round 1: 544 peptides, 117 chains. Longest chain 9 peptides. Score 0.255 Round 2: 736 peptides, 136 chains. Longest chain 15 peptides. Score 0.371 Round 3: 856 peptides, 140 chains. Longest chain 22 peptides. Score 0.465 Round 4: 904 peptides, 143 chains. Longest chain 24 peptides. Score 0.495 Round 5: 944 peptides, 137 chains. Longest chain 28 peptides. Score 0.548 Taking the results from Round 5 Chains 142, Residues 807, Estimated correctness of the model 0.0 % 11 chains (80 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29638 restraints for refining 12920 atoms. 26357 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2629 (Rfree = 0.000) for 12920 atoms. Found 39 (82 requested) and removed 104 (41 requested) atoms. Cycle 2: After refmac, R = 0.2471 (Rfree = 0.000) for 12638 atoms. Found 40 (82 requested) and removed 82 (41 requested) atoms. Cycle 3: After refmac, R = 0.2426 (Rfree = 0.000) for 12453 atoms. Found 35 (80 requested) and removed 79 (40 requested) atoms. Cycle 4: After refmac, R = 0.2355 (Rfree = 0.000) for 12327 atoms. Found 42 (79 requested) and removed 61 (39 requested) atoms. Cycle 5: After refmac, R = 0.2033 (Rfree = 0.000) for 12238 atoms. Found 20 (78 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.58 Search for helices and strands: 0 residues in 0 chains, 12605 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 12628 seeds are put forward Round 1: 745 peptides, 145 chains. Longest chain 15 peptides. Score 0.342 Round 2: 840 peptides, 139 chains. Longest chain 19 peptides. Score 0.455 Round 3: 862 peptides, 134 chains. Longest chain 17 peptides. Score 0.493 Round 4: 926 peptides, 141 chains. Longest chain 22 peptides. Score 0.520 Round 5: 898 peptides, 133 chains. Longest chain 30 peptides. Score 0.526 Taking the results from Round 5 Chains 136, Residues 765, Estimated correctness of the model 0.0 % 7 chains (65 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 27986 restraints for refining 12252 atoms. 24878 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2218 (Rfree = 0.000) for 12252 atoms. Found 43 (78 requested) and removed 105 (39 requested) atoms. Cycle 7: After refmac, R = 0.2061 (Rfree = 0.000) for 12095 atoms. Found 16 (78 requested) and removed 67 (39 requested) atoms. Cycle 8: After refmac, R = 0.2023 (Rfree = 0.000) for 12003 atoms. Found 28 (77 requested) and removed 59 (38 requested) atoms. Cycle 9: After refmac, R = 0.1957 (Rfree = 0.000) for 11931 atoms. Found 25 (76 requested) and removed 54 (38 requested) atoms. Cycle 10: After refmac, R = 0.1924 (Rfree = 0.000) for 11875 atoms. Found 20 (76 requested) and removed 51 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 12304 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 12335 seeds are put forward Round 1: 756 peptides, 142 chains. Longest chain 19 peptides. Score 0.365 Round 2: 865 peptides, 144 chains. Longest chain 17 peptides. Score 0.458 Round 3: 856 peptides, 136 chains. Longest chain 16 peptides. Score 0.480 Round 4: 860 peptides, 130 chains. Longest chain 18 peptides. Score 0.505 Round 5: 891 peptides, 130 chains. Longest chain 20 peptides. Score 0.531 Taking the results from Round 5 Chains 133, Residues 761, Estimated correctness of the model 0.0 % 10 chains (70 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20157 reflections ( 99.97 % complete ) and 27972 restraints for refining 12368 atoms. 24857 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 12368 atoms. Found 44 (79 requested) and removed 104 (39 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2086 (Rfree = 0.000) for 12239 atoms. Found 34 (78 requested) and removed 58 (39 requested) atoms. Cycle 13: After refmac, R = 0.2018 (Rfree = 0.000) for 12166 atoms. Found 31 (78 requested) and removed 64 (39 requested) atoms. Cycle 14: After refmac, R = 0.1959 (Rfree = 0.000) for 12104 atoms. Found 33 (77 requested) and removed 52 (38 requested) atoms. Cycle 15: After refmac, R = 0.1907 (Rfree = 0.000) for 12056 atoms. Found 32 (77 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 12437 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 12455 seeds are put forward Round 1: 674 peptides, 127 chains. Longest chain 14 peptides. Score 0.347 Round 2: 784 peptides, 131 chains. Longest chain 14 peptides. Score 0.436 Round 3: 811 peptides, 124 chains. Longest chain 17 peptides. Score 0.486 Round 4: 791 peptides, 119 chains. Longest chain 18 peptides. Score 0.488 Round 5: 838 peptides, 124 chains. Longest chain 16 peptides. Score 0.509 Taking the results from Round 5 Chains 124, Residues 714, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 28779 restraints for refining 12518 atoms. 26006 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2089 (Rfree = 0.000) for 12518 atoms. Found 55 (80 requested) and removed 97 (40 requested) atoms. Cycle 17: After refmac, R = 0.1939 (Rfree = 0.000) for 12418 atoms. Found 22 (80 requested) and removed 60 (40 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1888 (Rfree = 0.000) for 12353 atoms. Found 13 (79 requested) and removed 58 (39 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1838 (Rfree = 0.000) for 12282 atoms. Found 17 (78 requested) and removed 55 (39 requested) atoms. Cycle 20: After refmac, R = 0.1771 (Rfree = 0.000) for 12229 atoms. Found 12 (78 requested) and removed 52 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.57 Search for helices and strands: 0 residues in 0 chains, 12574 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 12597 seeds are put forward Round 1: 642 peptides, 119 chains. Longest chain 15 peptides. Score 0.349 Round 2: 728 peptides, 119 chains. Longest chain 15 peptides. Score 0.432 Round 3: 759 peptides, 123 chains. Longest chain 16 peptides. Score 0.444 Round 4: 758 peptides, 122 chains. Longest chain 19 peptides. Score 0.448 Round 5: 752 peptides, 120 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 5 Chains 120, Residues 632, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29911 restraints for refining 12674 atoms. 27489 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1986 (Rfree = 0.000) for 12674 atoms. Found 36 (81 requested) and removed 98 (40 requested) atoms. Cycle 22: After refmac, R = 0.1846 (Rfree = 0.000) for 12559 atoms. Found 34 (80 requested) and removed 60 (40 requested) atoms. Cycle 23: After refmac, R = 0.1804 (Rfree = 0.000) for 12510 atoms. Found 26 (80 requested) and removed 48 (40 requested) atoms. Cycle 24: After refmac, R = 0.1789 (Rfree = 0.000) for 12477 atoms. Found 28 (80 requested) and removed 54 (40 requested) atoms. Cycle 25: After refmac, R = 0.1811 (Rfree = 0.000) for 12434 atoms. Found 49 (79 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.62 Search for helices and strands: 0 residues in 0 chains, 12819 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 12846 seeds are put forward Round 1: 621 peptides, 119 chains. Longest chain 12 peptides. Score 0.328 Round 2: 746 peptides, 127 chains. Longest chain 12 peptides. Score 0.417 Round 3: 728 peptides, 121 chains. Longest chain 14 peptides. Score 0.424 Round 4: 758 peptides, 120 chains. Longest chain 14 peptides. Score 0.455 Round 5: 787 peptides, 130 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 4 Chains 122, Residues 638, Estimated correctness of the model 0.0 % 11 chains (62 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 29732 restraints for refining 12861 atoms. 27146 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1902 (Rfree = 0.000) for 12861 atoms. Found 43 (82 requested) and removed 102 (41 requested) atoms. Cycle 27: After refmac, R = 0.1764 (Rfree = 0.000) for 12750 atoms. Found 25 (82 requested) and removed 54 (41 requested) atoms. Cycle 28: After refmac, R = 0.1735 (Rfree = 0.000) for 12698 atoms. Found 22 (81 requested) and removed 52 (40 requested) atoms. Cycle 29: After refmac, R = 0.1691 (Rfree = 0.000) for 12653 atoms. Found 22 (81 requested) and removed 54 (40 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1714 (Rfree = 0.000) for 12612 atoms. Found 16 (80 requested) and removed 45 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 12943 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 12957 seeds are put forward Round 1: 662 peptides, 129 chains. Longest chain 11 peptides. Score 0.326 Round 2: 729 peptides, 127 chains. Longest chain 15 peptides. Score 0.401 Round 3: 750 peptides, 120 chains. Longest chain 14 peptides. Score 0.448 Round 4: 725 peptides, 120 chains. Longest chain 15 peptides. Score 0.425 Round 5: 735 peptides, 116 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 5 Chains 117, Residues 619, Estimated correctness of the model 0.0 % 8 chains (43 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20157 reflections ( 99.97 % complete ) and 30335 restraints for refining 12923 atoms. 27879 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1875 (Rfree = 0.000) for 12923 atoms. Found 52 (82 requested) and removed 64 (41 requested) atoms. Cycle 32: After refmac, R = 0.1762 (Rfree = 0.000) for 12868 atoms. Found 18 (82 requested) and removed 58 (41 requested) atoms. Cycle 33: After refmac, R = 0.1777 (Rfree = 0.000) for 12807 atoms. Found 27 (82 requested) and removed 48 (41 requested) atoms. Cycle 34: After refmac, R = 0.1818 (Rfree = 0.000) for 12771 atoms. Found 33 (82 requested) and removed 55 (41 requested) atoms. Cycle 35: After refmac, R = 0.1825 (Rfree = 0.000) for 12740 atoms. Found 43 (81 requested) and removed 58 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 13033 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 13055 seeds are put forward Round 1: 587 peptides, 113 chains. Longest chain 15 peptides. Score 0.319 Round 2: 641 peptides, 110 chains. Longest chain 21 peptides. Score 0.387 Round 3: 653 peptides, 110 chains. Longest chain 17 peptides. Score 0.398 Round 4: 641 peptides, 110 chains. Longest chain 19 peptides. Score 0.387 Round 5: 663 peptides, 110 chains. Longest chain 17 peptides. Score 0.408 Taking the results from Round 5 Chains 110, Residues 553, Estimated correctness of the model 0.0 % 8 chains (28 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 30738 restraints for refining 12923 atoms. 28587 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1891 (Rfree = 0.000) for 12923 atoms. Found 36 (82 requested) and removed 59 (41 requested) atoms. Cycle 37: After refmac, R = 0.1764 (Rfree = 0.000) for 12874 atoms. Found 36 (82 requested) and removed 50 (41 requested) atoms. Cycle 38: After refmac, R = 0.1838 (Rfree = 0.000) for 12842 atoms. Found 39 (82 requested) and removed 48 (41 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 12824 atoms. Found 49 (82 requested) and removed 51 (41 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1582 (Rfree = 0.000) for 12810 atoms. Found 13 (82 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 13144 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 13156 seeds are put forward Round 1: 575 peptides, 121 chains. Longest chain 15 peptides. Score 0.270 Round 2: 664 peptides, 118 chains. Longest chain 15 peptides. Score 0.375 Round 3: 664 peptides, 111 chains. Longest chain 17 peptides. Score 0.405 Round 4: 657 peptides, 114 chains. Longest chain 16 peptides. Score 0.385 Round 5: 662 peptides, 111 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 3 Chains 114, Residues 553, Estimated correctness of the model 0.0 % 9 chains (55 residues) have been docked in sequence ------------------------------------------------------ 20157 reflections ( 99.97 % complete ) and 30239 restraints for refining 12921 atoms. 27999 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1857 (Rfree = 0.000) for 12921 atoms. Found 47 (82 requested) and removed 60 (41 requested) atoms. Cycle 42: After refmac, R = 0.1854 (Rfree = 0.000) for 12873 atoms. Found 36 (82 requested) and removed 54 (41 requested) atoms. Cycle 43: After refmac, R = 0.1832 (Rfree = 0.000) for 12841 atoms. Found 37 (82 requested) and removed 63 (41 requested) atoms. Cycle 44: After refmac, R = 0.1898 (Rfree = 0.000) for 12801 atoms. Found 42 (82 requested) and removed 54 (41 requested) atoms. Cycle 45: After refmac, R = 0.1864 (Rfree = 0.000) for 12781 atoms. Found 32 (82 requested) and removed 49 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.59 Search for helices and strands: 0 residues in 0 chains, 13070 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 13087 seeds are put forward Round 1: 504 peptides, 107 chains. Longest chain 14 peptides. Score 0.256 Round 2: 586 peptides, 110 chains. Longest chain 11 peptides. Score 0.331 Round 3: 562 peptides, 99 chains. Longest chain 14 peptides. Score 0.355 Round 4: 588 peptides, 102 chains. Longest chain 17 peptides. Score 0.369 Round 5: 599 peptides, 102 chains. Longest chain 13 peptides. Score 0.379 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 102, Residues 497, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 102 chains (497 residues) following loop building 5 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20157 reflections ( 99.97 % complete ) and 30939 restraints for refining 12923 atoms. 29000 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2036 (Rfree = 0.000) for 12923 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2005 (Rfree = 0.000) for 12862 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1753 (Rfree = 0.000) for 12803 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1693 (Rfree = 0.000) for 12749 atoms. TimeTaking 114.62