Sun 23 Dec 23:53:28 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 1vl6-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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/1vl6-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 ============================================================ Sun 23 Dec 23:53:33 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/1vl6-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 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-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.90 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 13815 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3315 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3116 (Rfree = 0.000) for 13815 atoms. Found 104 (104 requested) and removed 218 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 13987 seeds are put forward NCS extension: 0 residues added, 13987 seeds are put forward Round 1: 693 peptides, 126 chains. Longest chain 20 peptides. Score 0.349 Round 2: 863 peptides, 128 chains. Longest chain 25 peptides. Score 0.480 Round 3: 907 peptides, 123 chains. Longest chain 29 peptides. Score 0.528 Round 4: 943 peptides, 121 chains. Longest chain 32 peptides. Score 0.558 Round 5: 954 peptides, 111 chains. Longest chain 37 peptides. Score 0.595 Taking the results from Round 5 Chains 116, Residues 843, Estimated correctness of the model 27.0 % 22 chains (289 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 22276 restraints for refining 11282 atoms. 17995 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2654 (Rfree = 0.000) for 11282 atoms. Found 85 (85 requested) and removed 143 (42 requested) atoms. Cycle 2: After refmac, R = 0.2475 (Rfree = 0.000) for 11038 atoms. Found 84 (84 requested) and removed 70 (42 requested) atoms. Cycle 3: After refmac, R = 0.2377 (Rfree = 0.000) for 10954 atoms. Found 64 (83 requested) and removed 67 (41 requested) atoms. Cycle 4: After refmac, R = 0.2362 (Rfree = 0.000) for 10883 atoms. Found 48 (82 requested) and removed 64 (41 requested) atoms. Cycle 5: After refmac, R = 0.2362 (Rfree = 0.000) for 10821 atoms. Found 48 (82 requested) and removed 58 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11196 seeds are put forward NCS extension: 6 residues added (17 deleted due to clashes), 11202 seeds are put forward Round 1: 884 peptides, 125 chains. Longest chain 29 peptides. Score 0.505 Round 2: 918 peptides, 109 chains. Longest chain 26 peptides. Score 0.578 Round 3: 978 peptides, 106 chains. Longest chain 34 peptides. Score 0.624 Round 4: 975 peptides, 114 chains. Longest chain 26 peptides. Score 0.599 Round 5: 960 peptides, 106 chains. Longest chain 29 peptides. Score 0.613 Taking the results from Round 3 Chains 117, Residues 872, Estimated correctness of the model 36.3 % 15 chains (166 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23214 restraints for refining 11284 atoms. 19220 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2523 (Rfree = 0.000) for 11284 atoms. Found 85 (85 requested) and removed 117 (42 requested) atoms. Cycle 7: After refmac, R = 0.2377 (Rfree = 0.000) for 11169 atoms. Found 61 (84 requested) and removed 75 (42 requested) atoms. Cycle 8: After refmac, R = 0.2309 (Rfree = 0.000) for 11117 atoms. Found 48 (84 requested) and removed 63 (42 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 11076 atoms. Found 65 (83 requested) and removed 55 (41 requested) atoms. Cycle 10: After refmac, R = 0.2073 (Rfree = 0.000) for 11054 atoms. Found 24 (83 requested) and removed 59 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 11400 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11417 seeds are put forward Round 1: 818 peptides, 113 chains. Longest chain 29 peptides. Score 0.496 Round 2: 894 peptides, 110 chains. Longest chain 29 peptides. Score 0.559 Round 3: 912 peptides, 110 chains. Longest chain 25 peptides. Score 0.571 Round 4: 896 peptides, 109 chains. Longest chain 32 peptides. Score 0.564 Round 5: 887 peptides, 105 chains. Longest chain 25 peptides. Score 0.570 Taking the results from Round 3 Chains 114, Residues 802, Estimated correctness of the model 18.9 % 12 chains (125 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 24407 restraints for refining 11285 atoms. 20898 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2335 (Rfree = 0.000) for 11285 atoms. Found 73 (85 requested) and removed 76 (42 requested) atoms. Cycle 12: After refmac, R = 0.2326 (Rfree = 0.000) for 11200 atoms. Found 59 (85 requested) and removed 63 (42 requested) atoms. Cycle 13: After refmac, R = 0.2086 (Rfree = 0.000) for 11126 atoms. Found 35 (84 requested) and removed 52 (42 requested) atoms. Cycle 14: After refmac, R = 0.1973 (Rfree = 0.000) for 11078 atoms. Found 25 (83 requested) and removed 51 (41 requested) atoms. Cycle 15: After refmac, R = 0.1906 (Rfree = 0.000) for 11030 atoms. Found 18 (83 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 11362 seeds are put forward NCS extension: 12 residues added (11 deleted due to clashes), 11374 seeds are put forward Round 1: 801 peptides, 119 chains. Longest chain 20 peptides. Score 0.463 Round 2: 877 peptides, 107 chains. Longest chain 25 peptides. Score 0.557 Round 3: 887 peptides, 105 chains. Longest chain 33 peptides. Score 0.570 Round 4: 904 peptides, 108 chains. Longest chain 26 peptides. Score 0.572 Round 5: 924 peptides, 111 chains. Longest chain 34 peptides. Score 0.576 Taking the results from Round 5 Chains 116, Residues 813, Estimated correctness of the model 20.7 % 10 chains (104 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 24440 restraints for refining 11289 atoms. 20949 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2348 (Rfree = 0.000) for 11289 atoms. Found 61 (85 requested) and removed 77 (42 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 11233 atoms. Found 52 (85 requested) and removed 52 (42 requested) atoms. Cycle 18: After refmac, R = 0.2149 (Rfree = 0.000) for 11204 atoms. Found 33 (84 requested) and removed 55 (42 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 11151 atoms. Found 19 (84 requested) and removed 50 (42 requested) atoms. Cycle 20: After refmac, R = 0.2012 (Rfree = 0.000) for 11110 atoms. Found 22 (83 requested) and removed 46 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 11439 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 11456 seeds are put forward Round 1: 827 peptides, 122 chains. Longest chain 24 peptides. Score 0.473 Round 2: 890 peptides, 114 chains. Longest chain 22 peptides. Score 0.544 Round 3: 882 peptides, 112 chains. Longest chain 33 peptides. Score 0.545 Round 4: 910 peptides, 105 chains. Longest chain 41 peptides. Score 0.585 Round 5: 916 peptides, 105 chains. Longest chain 50 peptides. Score 0.588 Taking the results from Round 5 Chains 115, Residues 811, Estimated correctness of the model 24.7 % 16 chains (170 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23396 restraints for refining 11286 atoms. 19638 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2361 (Rfree = 0.000) for 11286 atoms. Found 76 (85 requested) and removed 74 (42 requested) atoms. Cycle 22: After refmac, R = 0.2185 (Rfree = 0.000) for 11211 atoms. Found 54 (85 requested) and removed 55 (42 requested) atoms. Cycle 23: After refmac, R = 0.2113 (Rfree = 0.000) for 11176 atoms. Found 38 (84 requested) and removed 52 (42 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 11140 atoms. Found 34 (84 requested) and removed 50 (42 requested) atoms. Cycle 25: After refmac, R = 0.2050 (Rfree = 0.000) for 11103 atoms. Found 25 (83 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11460 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11477 seeds are put forward Round 1: 809 peptides, 130 chains. Longest chain 30 peptides. Score 0.431 Round 2: 878 peptides, 113 chains. Longest chain 26 peptides. Score 0.539 Round 3: 887 peptides, 111 chains. Longest chain 25 peptides. Score 0.551 Round 4: 915 peptides, 114 chains. Longest chain 29 peptides. Score 0.561 Round 5: 929 peptides, 117 chains. Longest chain 40 peptides. Score 0.561 Taking the results from Round 5 Chains 125, Residues 812, Estimated correctness of the model 15.4 % 12 chains (146 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23324 restraints for refining 11288 atoms. 19649 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2343 (Rfree = 0.000) for 11288 atoms. Found 83 (85 requested) and removed 62 (42 requested) atoms. Cycle 27: After refmac, R = 0.2203 (Rfree = 0.000) for 11253 atoms. Found 49 (85 requested) and removed 55 (42 requested) atoms. Cycle 28: After refmac, R = 0.2109 (Rfree = 0.000) for 11207 atoms. Found 44 (84 requested) and removed 54 (42 requested) atoms. Cycle 29: After refmac, R = 0.2023 (Rfree = 0.000) for 11169 atoms. Found 34 (84 requested) and removed 57 (42 requested) atoms. Cycle 30: After refmac, R = 0.2067 (Rfree = 0.000) for 11120 atoms. Found 53 (84 requested) and removed 54 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 11516 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 11534 seeds are put forward Round 1: 779 peptides, 125 chains. Longest chain 23 peptides. Score 0.425 Round 2: 851 peptides, 117 chains. Longest chain 23 peptides. Score 0.507 Round 3: 827 peptides, 113 chains. Longest chain 23 peptides. Score 0.503 Round 4: 870 peptides, 113 chains. Longest chain 22 peptides. Score 0.533 Round 5: 840 peptides, 109 chains. Longest chain 24 peptides. Score 0.525 Taking the results from Round 4 Chains 117, Residues 757, Estimated correctness of the model 5.3 % 8 chains (67 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24782 restraints for refining 11287 atoms. 21680 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2232 (Rfree = 0.000) for 11287 atoms. Found 61 (85 requested) and removed 57 (42 requested) atoms. Cycle 32: After refmac, R = 0.2076 (Rfree = 0.000) for 11260 atoms. Found 38 (85 requested) and removed 49 (42 requested) atoms. Cycle 33: After refmac, R = 0.2069 (Rfree = 0.000) for 11211 atoms. Found 41 (84 requested) and removed 54 (42 requested) atoms. Cycle 34: After refmac, R = 0.1978 (Rfree = 0.000) for 11170 atoms. Found 31 (84 requested) and removed 49 (42 requested) atoms. Cycle 35: After refmac, R = 0.1803 (Rfree = 0.000) for 11136 atoms. Found 8 (84 requested) and removed 48 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11475 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 11496 seeds are put forward Round 1: 761 peptides, 127 chains. Longest chain 22 peptides. Score 0.403 Round 2: 812 peptides, 115 chains. Longest chain 22 peptides. Score 0.485 Round 3: 856 peptides, 114 chains. Longest chain 40 peptides. Score 0.520 Round 4: 839 peptides, 111 chains. Longest chain 23 peptides. Score 0.518 Round 5: 858 peptides, 109 chains. Longest chain 26 peptides. Score 0.538 Taking the results from Round 5 Chains 112, Residues 749, Estimated correctness of the model 7.2 % 12 chains (99 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24423 restraints for refining 11287 atoms. 21214 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2214 (Rfree = 0.000) for 11287 atoms. Found 56 (85 requested) and removed 50 (42 requested) atoms. Cycle 37: After refmac, R = 0.2072 (Rfree = 0.000) for 11250 atoms. Found 36 (85 requested) and removed 46 (42 requested) atoms. Cycle 38: After refmac, R = 0.2041 (Rfree = 0.000) for 11211 atoms. Found 26 (84 requested) and removed 54 (42 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 11160 atoms. Found 36 (84 requested) and removed 47 (42 requested) atoms. Cycle 40: After refmac, R = 0.1941 (Rfree = 0.000) for 11131 atoms. Found 29 (84 requested) and removed 57 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 11474 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 11501 seeds are put forward Round 1: 686 peptides, 110 chains. Longest chain 17 peptides. Score 0.403 Round 2: 787 peptides, 106 chains. Longest chain 27 peptides. Score 0.496 Round 3: 776 peptides, 101 chains. Longest chain 27 peptides. Score 0.505 Round 4: 777 peptides, 110 chains. Longest chain 23 peptides. Score 0.475 Round 5: 778 peptides, 107 chains. Longest chain 29 peptides. Score 0.486 Taking the results from Round 3 Chains 104, Residues 675, Estimated correctness of the model 0.0 % 11 chains (115 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 24554 restraints for refining 11289 atoms. 21577 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2151 (Rfree = 0.000) for 11289 atoms. Found 59 (85 requested) and removed 60 (42 requested) atoms. Cycle 42: After refmac, R = 0.2074 (Rfree = 0.000) for 11262 atoms. Found 27 (85 requested) and removed 47 (42 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2026 (Rfree = 0.000) for 11225 atoms. Found 22 (84 requested) and removed 46 (42 requested) atoms. Cycle 44: After refmac, R = 0.1955 (Rfree = 0.000) for 11189 atoms. Found 21 (84 requested) and removed 52 (42 requested) atoms. Cycle 45: After refmac, R = 0.1939 (Rfree = 0.000) for 11139 atoms. Found 27 (84 requested) and removed 49 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 11496 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 11526 seeds are put forward Round 1: 653 peptides, 106 chains. Longest chain 18 peptides. Score 0.390 Round 2: 723 peptides, 102 chains. Longest chain 21 peptides. Score 0.461 Round 3: 733 peptides, 104 chains. Longest chain 21 peptides. Score 0.462 Round 4: 745 peptides, 95 chains. Longest chain 23 peptides. Score 0.503 Round 5: 748 peptides, 102 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 650, Estimated correctness of the model 0.0 % 10 chains (82 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 97 chains (650 residues) following loop building 10 chains (82 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26410 reflections ( 99.87 % complete ) and 25100 restraints for refining 11289 atoms. 22347 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2088 (Rfree = 0.000) for 11289 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2083 (Rfree = 0.000) for 11205 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 48: After refmac, R = 0.2053 (Rfree = 0.000) for 11141 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.2022 (Rfree = 0.000) for 11084 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 149.83