Tue 25 Dec 19:27:55 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 1vl6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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/1vl6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 ============================================================ Tue 25 Dec 19:28:05 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/1vl6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.4-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 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-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.4-parrot-hancs.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 13828 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3268 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3162 (Rfree = 0.000) for 13828 atoms. Found 104 (104 requested) and removed 110 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 14106 seeds are put forward NCS extension: 0 residues added, 14106 seeds are put forward Round 1: 645 peptides, 112 chains. Longest chain 21 peptides. Score 0.360 Round 2: 833 peptides, 126 chains. Longest chain 19 peptides. Score 0.464 Round 3: 892 peptides, 120 chains. Longest chain 26 peptides. Score 0.527 Round 4: 955 peptides, 127 chains. Longest chain 26 peptides. Score 0.548 Round 5: 924 peptides, 115 chains. Longest chain 25 peptides. Score 0.564 Taking the results from Round 5 Chains 124, Residues 809, Estimated correctness of the model 16.5 % 17 chains (189 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 23788 restraints for refining 11280 atoms. 20017 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2867 (Rfree = 0.000) for 11280 atoms. Found 85 (85 requested) and removed 97 (42 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2495 (Rfree = 0.000) for 11020 atoms. Found 74 (85 requested) and removed 67 (42 requested) atoms. Cycle 3: After refmac, R = 0.2338 (Rfree = 0.000) for 10898 atoms. Found 62 (83 requested) and removed 57 (41 requested) atoms. Cycle 4: After refmac, R = 0.2311 (Rfree = 0.000) for 10829 atoms. Found 59 (82 requested) and removed 64 (41 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2309 (Rfree = 0.000) for 10790 atoms. Found 62 (81 requested) and removed 58 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11225 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 11251 seeds are put forward Round 1: 824 peptides, 121 chains. Longest chain 20 peptides. Score 0.474 Round 2: 928 peptides, 111 chains. Longest chain 33 peptides. Score 0.578 Round 3: 939 peptides, 112 chains. Longest chain 44 peptides. Score 0.583 Round 4: 964 peptides, 118 chains. Longest chain 26 peptides. Score 0.581 Round 5: 943 peptides, 112 chains. Longest chain 33 peptides. Score 0.585 Taking the results from Round 5 Chains 119, Residues 831, Estimated correctness of the model 23.7 % 9 chains (113 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24111 restraints for refining 11287 atoms. 20472 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2498 (Rfree = 0.000) for 11287 atoms. Found 85 (85 requested) and removed 80 (42 requested) atoms. Cycle 7: After refmac, R = 0.2426 (Rfree = 0.000) for 11189 atoms. Found 77 (85 requested) and removed 65 (42 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 11157 atoms. Found 53 (84 requested) and removed 65 (42 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2228 (Rfree = 0.000) for 11106 atoms. Found 47 (84 requested) and removed 49 (42 requested) atoms. Cycle 10: After refmac, R = 0.2180 (Rfree = 0.000) for 11078 atoms. Found 42 (83 requested) and removed 51 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 11519 seeds are put forward NCS extension: 23 residues added (12 deleted due to clashes), 11542 seeds are put forward Round 1: 829 peptides, 124 chains. Longest chain 21 peptides. Score 0.467 Round 2: 924 peptides, 117 chains. Longest chain 23 peptides. Score 0.558 Round 3: 938 peptides, 114 chains. Longest chain 27 peptides. Score 0.576 Round 4: 917 peptides, 105 chains. Longest chain 34 peptides. Score 0.589 Round 5: 952 peptides, 114 chains. Longest chain 29 peptides. Score 0.585 Taking the results from Round 4 Chains 108, Residues 812, Estimated correctness of the model 25.0 % 8 chains (134 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 23771 restraints for refining 11286 atoms. 20073 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 11286 atoms. Found 53 (85 requested) and removed 71 (42 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2303 (Rfree = 0.000) for 11192 atoms. Found 37 (85 requested) and removed 59 (42 requested) atoms. Cycle 13: After refmac, R = 0.2299 (Rfree = 0.000) for 11126 atoms. Found 37 (84 requested) and removed 54 (42 requested) atoms. Cycle 14: After refmac, R = 0.2237 (Rfree = 0.000) for 11086 atoms. Found 30 (83 requested) and removed 59 (41 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 11036 atoms. Found 32 (83 requested) and removed 54 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11459 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 11474 seeds are put forward Round 1: 818 peptides, 122 chains. Longest chain 22 peptides. Score 0.466 Round 2: 881 peptides, 117 chains. Longest chain 26 peptides. Score 0.528 Round 3: 886 peptides, 114 chains. Longest chain 18 peptides. Score 0.541 Round 4: 903 peptides, 111 chains. Longest chain 22 peptides. Score 0.562 Round 5: 901 peptides, 107 chains. Longest chain 25 peptides. Score 0.573 Taking the results from Round 5 Chains 117, Residues 794, Estimated correctness of the model 19.6 % 12 chains (122 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24049 restraints for refining 11288 atoms. 20563 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2409 (Rfree = 0.000) for 11288 atoms. Found 59 (85 requested) and removed 64 (42 requested) atoms. Cycle 17: After refmac, R = 0.2260 (Rfree = 0.000) for 11226 atoms. Found 46 (85 requested) and removed 49 (42 requested) atoms. Cycle 18: After refmac, R = 0.2247 (Rfree = 0.000) for 11182 atoms. Found 41 (84 requested) and removed 52 (42 requested) atoms. Cycle 19: After refmac, R = 0.2199 (Rfree = 0.000) for 11139 atoms. Found 46 (84 requested) and removed 50 (42 requested) atoms. Cycle 20: After refmac, R = 0.2160 (Rfree = 0.000) for 11113 atoms. Found 33 (84 requested) and removed 55 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11453 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 11477 seeds are put forward Round 1: 829 peptides, 127 chains. Longest chain 25 peptides. Score 0.457 Round 2: 912 peptides, 123 chains. Longest chain 34 peptides. Score 0.531 Round 3: 928 peptides, 121 chains. Longest chain 27 peptides. Score 0.548 Round 4: 911 peptides, 116 chains. Longest chain 36 peptides. Score 0.552 Round 5: 886 peptides, 115 chains. Longest chain 33 peptides. Score 0.538 Taking the results from Round 4 Chains 120, Residues 795, Estimated correctness of the model 12.2 % 9 chains (105 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24289 restraints for refining 11286 atoms. 20830 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2362 (Rfree = 0.000) for 11286 atoms. Found 55 (85 requested) and removed 58 (42 requested) atoms. Cycle 22: After refmac, R = 0.2221 (Rfree = 0.000) for 11214 atoms. Found 37 (85 requested) and removed 54 (42 requested) atoms. Cycle 23: After refmac, R = 0.2131 (Rfree = 0.000) for 11156 atoms. Found 30 (84 requested) and removed 45 (42 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2085 (Rfree = 0.000) for 11111 atoms. Found 22 (84 requested) and removed 49 (42 requested) atoms. Cycle 25: After refmac, R = 0.2014 (Rfree = 0.000) for 11060 atoms. Found 25 (83 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 11394 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 11407 seeds are put forward Round 1: 785 peptides, 129 chains. Longest chain 22 peptides. Score 0.416 Round 2: 879 peptides, 124 chains. Longest chain 31 peptides. Score 0.505 Round 3: 886 peptides, 119 chains. Longest chain 23 peptides. Score 0.526 Round 4: 878 peptides, 119 chains. Longest chain 26 peptides. Score 0.520 Round 5: 847 peptides, 116 chains. Longest chain 22 peptides. Score 0.507 Taking the results from Round 3 Chains 123, Residues 767, Estimated correctness of the model 2.7 % 12 chains (124 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 24503 restraints for refining 11289 atoms. 21114 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2301 (Rfree = 0.000) for 11289 atoms. Found 69 (85 requested) and removed 61 (42 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2140 (Rfree = 0.000) for 11229 atoms. Found 44 (85 requested) and removed 52 (42 requested) atoms. Cycle 28: After refmac, R = 0.2147 (Rfree = 0.000) for 11201 atoms. Found 31 (84 requested) and removed 48 (42 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 11162 atoms. Found 27 (84 requested) and removed 51 (42 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2059 (Rfree = 0.000) for 11116 atoms. Found 20 (84 requested) and removed 51 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11475 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11499 seeds are put forward Round 1: 761 peptides, 123 chains. Longest chain 19 peptides. Score 0.417 Round 2: 831 peptides, 122 chains. Longest chain 19 peptides. Score 0.476 Round 3: 844 peptides, 111 chains. Longest chain 23 peptides. Score 0.521 Round 4: 861 peptides, 120 chains. Longest chain 32 peptides. Score 0.505 Round 5: 854 peptides, 117 chains. Longest chain 27 peptides. Score 0.509 Taking the results from Round 3 Chains 114, Residues 733, Estimated correctness of the model 0.8 % 12 chains (104 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 24709 restraints for refining 11288 atoms. 21509 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2297 (Rfree = 0.000) for 11288 atoms. Found 52 (85 requested) and removed 53 (42 requested) atoms. Cycle 32: After refmac, R = 0.2214 (Rfree = 0.000) for 11229 atoms. Found 49 (85 requested) and removed 44 (42 requested) atoms. Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 11200 atoms. Found 25 (84 requested) and removed 49 (42 requested) atoms. Cycle 34: After refmac, R = 0.2201 (Rfree = 0.000) for 11140 atoms. Found 43 (84 requested) and removed 48 (42 requested) atoms. Cycle 35: After refmac, R = 0.2201 (Rfree = 0.000) for 11114 atoms. Found 42 (84 requested) and removed 55 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 11492 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 11519 seeds are put forward Round 1: 711 peptides, 121 chains. Longest chain 16 peptides. Score 0.383 Round 2: 785 peptides, 111 chains. Longest chain 23 peptides. Score 0.478 Round 3: 760 peptides, 109 chains. Longest chain 27 peptides. Score 0.466 Round 4: 807 peptides, 114 chains. Longest chain 21 peptides. Score 0.484 Round 5: 803 peptides, 118 chains. Longest chain 25 peptides. Score 0.468 Taking the results from Round 4 Chains 118, Residues 693, Estimated correctness of the model 0.0 % 15 chains (106 residues) have been docked in sequence ------------------------------------------------------ 26410 reflections ( 99.87 % complete ) and 25022 restraints for refining 11288 atoms. 22016 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2322 (Rfree = 0.000) for 11288 atoms. Found 66 (85 requested) and removed 58 (42 requested) atoms. Cycle 37: After refmac, R = 0.2165 (Rfree = 0.000) for 11246 atoms. Found 40 (85 requested) and removed 49 (42 requested) atoms. Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 11215 atoms. Found 42 (84 requested) and removed 50 (42 requested) atoms. Cycle 39: After refmac, R = 0.2049 (Rfree = 0.000) for 11190 atoms. Found 27 (84 requested) and removed 50 (42 requested) atoms. Cycle 40: After refmac, R = 0.2074 (Rfree = 0.000) for 11148 atoms. Found 42 (84 requested) and removed 46 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11588 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 11615 seeds are put forward Round 1: 710 peptides, 121 chains. Longest chain 20 peptides. Score 0.382 Round 2: 765 peptides, 118 chains. Longest chain 22 peptides. Score 0.438 Round 3: 778 peptides, 115 chains. Longest chain 21 peptides. Score 0.459 Round 4: 794 peptides, 108 chains. Longest chain 24 peptides. Score 0.495 Round 5: 796 peptides, 112 chains. Longest chain 23 peptides. Score 0.483 Taking the results from Round 4 Chains 112, Residues 686, Estimated correctness of the model 0.0 % 16 chains (126 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 26410 reflections ( 99.87 % complete ) and 24517 restraints for refining 11287 atoms. 21445 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2235 (Rfree = 0.000) for 11287 atoms. Found 45 (85 requested) and removed 59 (42 requested) atoms. Cycle 42: After refmac, R = 0.2178 (Rfree = 0.000) for 11224 atoms. Found 38 (85 requested) and removed 49 (42 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2113 (Rfree = 0.000) for 11189 atoms. Found 29 (84 requested) and removed 48 (42 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2082 (Rfree = 0.000) for 11152 atoms. Found 34 (84 requested) and removed 46 (42 requested) atoms. Cycle 45: After refmac, R = 0.2088 (Rfree = 0.000) for 11129 atoms. Found 44 (84 requested) and removed 54 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 11477 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 11513 seeds are put forward Round 1: 666 peptides, 120 chains. Longest chain 20 peptides. Score 0.348 Round 2: 776 peptides, 114 chains. Longest chain 22 peptides. Score 0.461 Round 3: 783 peptides, 118 chains. Longest chain 18 peptides. Score 0.452 Round 4: 788 peptides, 112 chains. Longest chain 31 peptides. Score 0.477 Round 5: 794 peptides, 113 chains. Longest chain 22 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 115, Residues 681, Estimated correctness of the model 0.0 % 13 chains (114 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 73 B and 87 B 114 chains (689 residues) following loop building 12 chains (127 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26410 reflections ( 99.87 % complete ) and 24473 restraints for refining 11288 atoms. 21423 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2312 (Rfree = 0.000) for 11288 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2273 (Rfree = 0.000) for 11193 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 48: After refmac, R = 0.2254 (Rfree = 0.000) for 11126 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.2231 (Rfree = 0.000) for 11068 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 22:14:29 GMT 2018 Job finished. TimeTaking 166.56