null Mon 24 Dec 07:40:19 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 1vl6-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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/1vl6-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 07:40:24 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/1vl6-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 1304 and 0 Target number of residues in the AU: 1304 Target solvent content: 0.6390 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.4-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.85 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: 124.815 3.400 Wilson plot Bfac: 71.43 26410 reflections ( 99.87 % complete ) and 0 restraints for refining 13787 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3320 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3187 (Rfree = 0.000) for 13787 atoms. Found 104 (104 requested) and removed 92 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 14090 seeds are put forward NCS extension: 0 residues added, 14090 seeds are put forward Round 1: 662 peptides, 117 chains. Longest chain 15 peptides. Score 0.356 Round 2: 843 peptides, 124 chains. Longest chain 22 peptides. Score 0.478 Round 3: 899 peptides, 116 chains. Longest chain 27 peptides. Score 0.544 Round 4: 933 peptides, 117 chains. Longest chain 25 peptides. Score 0.564 Round 5: 913 peptides, 97 chains. Longest chain 28 peptides. Score 0.610 Taking the results from Round 5 Chains 114, Residues 816, Estimated correctness of the model 31.9 % 18 chains (205 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23403 restraints for refining 11284 atoms. 19522 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2688 (Rfree = 0.000) for 11284 atoms. Found 85 (85 requested) and removed 100 (42 requested) atoms. Cycle 2: After refmac, R = 0.2536 (Rfree = 0.000) for 11100 atoms. Found 85 (85 requested) and removed 117 (42 requested) atoms. Cycle 3: After refmac, R = 0.2418 (Rfree = 0.000) for 10981 atoms. Found 70 (83 requested) and removed 81 (41 requested) atoms. Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 10906 atoms. Found 60 (82 requested) and removed 85 (41 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 10831 atoms. Found 50 (82 requested) and removed 73 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 11175 seeds are put forward NCS extension: 12 residues added (11 deleted due to clashes), 11187 seeds are put forward Round 1: 825 peptides, 124 chains. Longest chain 19 peptides. Score 0.464 Round 2: 862 peptides, 115 chains. Longest chain 20 peptides. Score 0.521 Round 3: 920 peptides, 119 chains. Longest chain 32 peptides. Score 0.549 Round 4: 927 peptides, 113 chains. Longest chain 26 peptides. Score 0.572 Round 5: 921 peptides, 114 chains. Longest chain 31 peptides. Score 0.565 Taking the results from Round 4 Chains 124, Residues 814, Estimated correctness of the model 19.3 % 15 chains (138 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24165 restraints for refining 11287 atoms. 20613 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2434 (Rfree = 0.000) for 11287 atoms. Found 69 (85 requested) and removed 94 (42 requested) atoms. Cycle 7: After refmac, R = 0.2314 (Rfree = 0.000) for 11178 atoms. Found 44 (85 requested) and removed 67 (42 requested) atoms. Cycle 8: After refmac, R = 0.2244 (Rfree = 0.000) for 11104 atoms. Found 51 (84 requested) and removed 65 (42 requested) atoms. Cycle 9: After refmac, R = 0.2243 (Rfree = 0.000) for 11051 atoms. Found 57 (83 requested) and removed 59 (41 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 11013 atoms. Found 46 (83 requested) and removed 54 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11439 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 11457 seeds are put forward Round 1: 871 peptides, 135 chains. Longest chain 23 peptides. Score 0.463 Round 2: 925 peptides, 111 chains. Longest chain 38 peptides. Score 0.576 Round 3: 926 peptides, 120 chains. Longest chain 31 peptides. Score 0.550 Round 4: 921 peptides, 114 chains. Longest chain 27 peptides. Score 0.565 Round 5: 950 peptides, 116 chains. Longest chain 31 peptides. Score 0.578 Taking the results from Round 5 Chains 124, Residues 834, Estimated correctness of the model 21.3 % 13 chains (187 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23492 restraints for refining 11287 atoms. 19563 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2418 (Rfree = 0.000) for 11287 atoms. Found 71 (85 requested) and removed 70 (42 requested) atoms. Cycle 12: After refmac, R = 0.2345 (Rfree = 0.000) for 11191 atoms. Found 58 (85 requested) and removed 67 (42 requested) atoms. Cycle 13: After refmac, R = 0.2253 (Rfree = 0.000) for 11138 atoms. Found 35 (84 requested) and removed 52 (42 requested) atoms. Cycle 14: After refmac, R = 0.2241 (Rfree = 0.000) for 11083 atoms. Found 38 (83 requested) and removed 54 (41 requested) atoms. Cycle 15: After refmac, R = 0.2222 (Rfree = 0.000) for 11039 atoms. Found 46 (83 requested) and removed 57 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11420 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 11436 seeds are put forward Round 1: 806 peptides, 122 chains. Longest chain 32 peptides. Score 0.457 Round 2: 905 peptides, 120 chains. Longest chain 24 peptides. Score 0.536 Round 3: 918 peptides, 116 chains. Longest chain 29 peptides. Score 0.557 Round 4: 927 peptides, 124 chains. Longest chain 20 peptides. Score 0.538 Round 5: 946 peptides, 121 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 5 Chains 131, Residues 825, Estimated correctness of the model 15.1 % 12 chains (115 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24122 restraints for refining 11286 atoms. 20546 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2416 (Rfree = 0.000) for 11286 atoms. Found 77 (85 requested) and removed 74 (42 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 11235 atoms. Found 55 (85 requested) and removed 56 (42 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 11204 atoms. Found 54 (84 requested) and removed 46 (42 requested) atoms. Cycle 19: After refmac, R = 0.2203 (Rfree = 0.000) for 11197 atoms. Found 47 (84 requested) and removed 50 (42 requested) atoms. Cycle 20: After refmac, R = 0.2141 (Rfree = 0.000) for 11175 atoms. Found 31 (84 requested) and removed 50 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11544 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 11555 seeds are put forward Round 1: 811 peptides, 119 chains. Longest chain 19 peptides. Score 0.471 Round 2: 878 peptides, 113 chains. Longest chain 26 peptides. Score 0.539 Round 3: 898 peptides, 111 chains. Longest chain 25 peptides. Score 0.559 Round 4: 868 peptides, 103 chains. Longest chain 29 peptides. Score 0.563 Round 5: 904 peptides, 111 chains. Longest chain 44 peptides. Score 0.563 Taking the results from Round 5 Chains 119, Residues 793, Estimated correctness of the model 16.1 % 17 chains (188 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23556 restraints for refining 11288 atoms. 19817 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2525 (Rfree = 0.000) for 11288 atoms. Found 83 (85 requested) and removed 76 (42 requested) atoms. Cycle 22: After refmac, R = 0.2415 (Rfree = 0.000) for 11219 atoms. Found 70 (85 requested) and removed 66 (42 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 11180 atoms. Found 49 (84 requested) and removed 47 (42 requested) atoms. Cycle 24: After refmac, R = 0.2252 (Rfree = 0.000) for 11160 atoms. Found 41 (84 requested) and removed 53 (42 requested) atoms. Cycle 25: After refmac, R = 0.2250 (Rfree = 0.000) for 11124 atoms. Found 66 (84 requested) and removed 60 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11515 seeds are put forward NCS extension: 34 residues added (7 deleted due to clashes), 11549 seeds are put forward Round 1: 793 peptides, 133 chains. Longest chain 22 peptides. Score 0.408 Round 2: 868 peptides, 118 chains. Longest chain 23 peptides. Score 0.516 Round 3: 838 peptides, 110 chains. Longest chain 40 peptides. Score 0.520 Round 4: 877 peptides, 111 chains. Longest chain 32 peptides. Score 0.545 Round 5: 849 peptides, 119 chains. Longest chain 33 peptides. Score 0.499 Taking the results from Round 4 Chains 114, Residues 766, Estimated correctness of the model 9.7 % 9 chains (103 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24861 restraints for refining 11289 atoms. 21557 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2323 (Rfree = 0.000) for 11289 atoms. Found 85 (85 requested) and removed 61 (42 requested) atoms. Cycle 27: After refmac, R = 0.2194 (Rfree = 0.000) for 11251 atoms. Found 59 (85 requested) and removed 50 (42 requested) atoms. Cycle 28: After refmac, R = 0.2129 (Rfree = 0.000) for 11226 atoms. Found 46 (85 requested) and removed 49 (42 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 11192 atoms. Found 57 (84 requested) and removed 45 (42 requested) atoms. Cycle 30: After refmac, R = 0.2017 (Rfree = 0.000) for 11174 atoms. Found 36 (84 requested) and removed 48 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 11539 seeds are put forward NCS extension: 15 residues added (9 deleted due to clashes), 11554 seeds are put forward Round 1: 778 peptides, 126 chains. Longest chain 28 peptides. Score 0.420 Round 2: 832 peptides, 121 chains. Longest chain 31 peptides. Score 0.480 Round 3: 837 peptides, 114 chains. Longest chain 27 peptides. Score 0.507 Round 4: 849 peptides, 115 chains. Longest chain 29 peptides. Score 0.512 Round 5: 857 peptides, 109 chains. Longest chain 41 peptides. Score 0.537 Taking the results from Round 5 Chains 113, Residues 748, Estimated correctness of the model 6.8 % 7 chains (104 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24408 restraints for refining 11285 atoms. 21163 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2319 (Rfree = 0.000) for 11285 atoms. Found 62 (85 requested) and removed 62 (42 requested) atoms. Cycle 32: After refmac, R = 0.2205 (Rfree = 0.000) for 11227 atoms. Found 50 (85 requested) and removed 51 (42 requested) atoms. Cycle 33: After refmac, R = 0.2139 (Rfree = 0.000) for 11186 atoms. Found 40 (84 requested) and removed 52 (42 requested) atoms. Cycle 34: After refmac, R = 0.2116 (Rfree = 0.000) for 11153 atoms. Found 38 (84 requested) and removed 46 (42 requested) atoms. Cycle 35: After refmac, R = 0.1913 (Rfree = 0.000) for 11119 atoms. Found 16 (84 requested) and removed 50 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 11451 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11471 seeds are put forward Round 1: 755 peptides, 128 chains. Longest chain 22 peptides. Score 0.394 Round 2: 791 peptides, 113 chains. Longest chain 22 peptides. Score 0.476 Round 3: 790 peptides, 112 chains. Longest chain 28 peptides. Score 0.478 Round 4: 804 peptides, 117 chains. Longest chain 21 peptides. Score 0.472 Round 5: 809 peptides, 114 chains. Longest chain 26 peptides. Score 0.486 Taking the results from Round 5 Chains 115, Residues 695, Estimated correctness of the model 0.0 % 9 chains (68 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 25345 restraints for refining 11287 atoms. 22463 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2421 (Rfree = 0.000) for 11287 atoms. Found 75 (85 requested) and removed 61 (42 requested) atoms. Cycle 37: After refmac, R = 0.2099 (Rfree = 0.000) for 11236 atoms. Found 44 (85 requested) and removed 55 (42 requested) atoms. Cycle 38: After refmac, R = 0.2119 (Rfree = 0.000) for 11196 atoms. Found 48 (84 requested) and removed 47 (42 requested) atoms. Cycle 39: After refmac, R = 0.1972 (Rfree = 0.000) for 11180 atoms. Found 29 (84 requested) and removed 50 (42 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 11143 atoms. Found 14 (84 requested) and removed 49 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11496 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 11517 seeds are put forward Round 1: 709 peptides, 125 chains. Longest chain 21 peptides. Score 0.366 Round 2: 801 peptides, 120 chains. Longest chain 29 peptides. Score 0.460 Round 3: 823 peptides, 114 chains. Longest chain 29 peptides. Score 0.496 Round 4: 842 peptides, 117 chains. Longest chain 27 peptides. Score 0.501 Round 5: 801 peptides, 114 chains. Longest chain 20 peptides. Score 0.480 Taking the results from Round 4 Chains 121, Residues 725, Estimated correctness of the model 0.0 % 9 chains (79 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24347 restraints for refining 11288 atoms. 21285 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2160 (Rfree = 0.000) for 11288 atoms. Found 59 (85 requested) and removed 54 (42 requested) atoms. Cycle 42: After refmac, R = 0.2052 (Rfree = 0.000) for 11245 atoms. Found 50 (85 requested) and removed 49 (42 requested) atoms. Cycle 43: After refmac, R = 0.2005 (Rfree = 0.000) for 11224 atoms. Found 49 (84 requested) and removed 48 (42 requested) atoms. Cycle 44: After refmac, R = 0.1918 (Rfree = 0.000) for 11198 atoms. Found 34 (84 requested) and removed 45 (42 requested) atoms. Cycle 45: After refmac, R = 0.1870 (Rfree = 0.000) for 11172 atoms. Found 27 (84 requested) and removed 52 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11516 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 11542 seeds are put forward Round 1: 663 peptides, 115 chains. Longest chain 16 peptides. Score 0.364 Round 2: 726 peptides, 109 chains. Longest chain 22 peptides. Score 0.439 Round 3: 776 peptides, 113 chains. Longest chain 20 peptides. Score 0.464 Round 4: 758 peptides, 110 chains. Longest chain 23 peptides. Score 0.461 Round 5: 745 peptides, 101 chains. Longest chain 22 peptides. Score 0.482 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 644, Estimated correctness of the model 0.0 % 7 chains (47 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 101 chains (644 residues) following loop building 7 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26410 reflections ( 99.87 % complete ) and 25544 restraints for refining 11287 atoms. 22931 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2198 (Rfree = 0.000) for 11287 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2125 (Rfree = 0.000) for 11208 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 11154 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.1979 (Rfree = 0.000) for 11102 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:48:10 GMT 2018 Job finished. TimeTaking 127.85 Used memory is bytes: 12086936