null Sun 23 Dec 22:22:52 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 2hhz-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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/2hhz-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 ============================================================ Sun 23 Dec 22:23:00 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/2hhz-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 97 and 0 Target number of residues in the AU: 97 Target solvent content: 0.6437 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 150 Adjusted target solvent content: 0.45 Input MTZ file: 2hhz-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: 96 Cell parameters: 71.030 71.030 58.410 90.000 90.000 90.000 Input sequence file: 2hhz-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1200 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.226 3.400 Wilson plot Bfac: 73.07 2265 reflections ( 99.52 % complete ) and 0 restraints for refining 1329 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3395 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2983 (Rfree = 0.000) for 1329 atoms. Found 10 (10 requested) and removed 34 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.65 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 47 peptides, 8 chains. Longest chain 9 peptides. Score 0.364 Round 2: 67 peptides, 11 chains. Longest chain 13 peptides. Score 0.440 Round 3: 80 peptides, 11 chains. Longest chain 19 peptides. Score 0.563 Round 4: 93 peptides, 13 chains. Longest chain 18 peptides. Score 0.597 Round 5: 92 peptides, 13 chains. Longest chain 16 peptides. Score 0.589 Taking the results from Round 4 Chains 13, Residues 80, Estimated correctness of the model 27.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2487 restraints for refining 1091 atoms. 2180 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2706 (Rfree = 0.000) for 1091 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.2403 (Rfree = 0.000) for 1069 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 1058 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2177 (Rfree = 0.000) for 1054 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2115 (Rfree = 0.000) for 1051 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.63 Search for helices and strands: 0 residues in 0 chains, 1095 seeds are put forward Round 1: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.496 Round 2: 89 peptides, 11 chains. Longest chain 21 peptides. Score 0.635 Round 3: 95 peptides, 12 chains. Longest chain 18 peptides. Score 0.646 Round 4: 95 peptides, 12 chains. Longest chain 22 peptides. Score 0.646 Round 5: 94 peptides, 13 chains. Longest chain 19 peptides. Score 0.605 Taking the results from Round 4 Chains 12, Residues 83, Estimated correctness of the model 43.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2388 restraints for refining 1084 atoms. 2068 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2690 (Rfree = 0.000) for 1084 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2456 (Rfree = 0.000) for 1078 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2434 (Rfree = 0.000) for 1073 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2412 (Rfree = 0.000) for 1069 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2389 (Rfree = 0.000) for 1062 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 1086 seeds are put forward Round 1: 90 peptides, 12 chains. Longest chain 18 peptides. Score 0.609 Round 2: 90 peptides, 13 chains. Longest chain 19 peptides. Score 0.573 Round 3: 100 peptides, 12 chains. Longest chain 26 peptides. Score 0.680 Round 4: 98 peptides, 12 chains. Longest chain 22 peptides. Score 0.667 Round 5: 106 peptides, 12 chains. Longest chain 26 peptides. Score 0.717 Taking the results from Round 5 Chains 12, Residues 94, Estimated correctness of the model 62.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2266 restraints for refining 1090 atoms. 1902 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2626 (Rfree = 0.000) for 1090 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 12: After refmac, R = 0.2487 (Rfree = 0.000) for 1085 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.2361 (Rfree = 0.000) for 1081 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2307 (Rfree = 0.000) for 1076 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2282 (Rfree = 0.000) for 1074 atoms. Found 1 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1104 seeds are put forward Round 1: 81 peptides, 11 chains. Longest chain 17 peptides. Score 0.572 Round 2: 86 peptides, 12 chains. Longest chain 15 peptides. Score 0.576 Round 3: 95 peptides, 11 chains. Longest chain 18 peptides. Score 0.677 Round 4: 96 peptides, 10 chains. Longest chain 21 peptides. Score 0.713 Round 5: 99 peptides, 11 chains. Longest chain 18 peptides. Score 0.703 Taking the results from Round 4 Chains 10, Residues 86, Estimated correctness of the model 61.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2358 restraints for refining 1091 atoms. 2024 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2350 (Rfree = 0.000) for 1091 atoms. Found 4 (7 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2166 (Rfree = 0.000) for 1087 atoms. Found 4 (7 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2108 (Rfree = 0.000) for 1086 atoms. Found 1 (7 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2087 (Rfree = 0.000) for 1080 atoms. Found 2 (7 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2042 (Rfree = 0.000) for 1078 atoms. Found 1 (7 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 1097 seeds are put forward Round 1: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.512 Round 2: 92 peptides, 12 chains. Longest chain 15 peptides. Score 0.624 Round 3: 92 peptides, 11 chains. Longest chain 21 peptides. Score 0.657 Round 4: 83 peptides, 9 chains. Longest chain 21 peptides. Score 0.658 Round 5: 90 peptides, 10 chains. Longest chain 21 peptides. Score 0.675 Taking the results from Round 5 Chains 12, Residues 80, Estimated correctness of the model 51.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2291 restraints for refining 1091 atoms. 1940 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2361 (Rfree = 0.000) for 1091 atoms. Found 6 (6 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.2054 (Rfree = 0.000) for 1082 atoms. Found 1 (6 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.1999 (Rfree = 0.000) for 1076 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.1916 (Rfree = 0.000) for 1073 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1867 (Rfree = 0.000) for 1070 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 1104 seeds are put forward Round 1: 69 peptides, 10 chains. Longest chain 16 peptides. Score 0.503 Round 2: 76 peptides, 9 chains. Longest chain 20 peptides. Score 0.605 Round 3: 71 peptides, 9 chains. Longest chain 18 peptides. Score 0.563 Round 4: 83 peptides, 10 chains. Longest chain 20 peptides. Score 0.624 Round 5: 81 peptides, 11 chains. Longest chain 13 peptides. Score 0.572 Taking the results from Round 4 Chains 10, Residues 73, Estimated correctness of the model 36.3 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2189 restraints for refining 1091 atoms. 1831 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 1091 atoms. Found 1 (6 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2185 (Rfree = 0.000) for 1075 atoms. Found 1 (6 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2173 (Rfree = 0.000) for 1070 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2074 (Rfree = 0.000) for 1068 atoms. Found 3 (6 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2076 (Rfree = 0.000) for 1066 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 1086 seeds are put forward Round 1: 77 peptides, 12 chains. Longest chain 13 peptides. Score 0.496 Round 2: 80 peptides, 8 chains. Longest chain 22 peptides. Score 0.670 Round 3: 86 peptides, 9 chains. Longest chain 18 peptides. Score 0.679 Round 4: 84 peptides, 8 chains. Longest chain 22 peptides. Score 0.697 Round 5: 80 peptides, 9 chains. Longest chain 22 peptides. Score 0.636 Taking the results from Round 4 Chains 8, Residues 76, Estimated correctness of the model 57.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2335 restraints for refining 1078 atoms. 2039 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2150 (Rfree = 0.000) for 1078 atoms. Found 5 (6 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2045 (Rfree = 0.000) for 1075 atoms. Found 5 (6 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.1996 (Rfree = 0.000) for 1076 atoms. Found 2 (6 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.1954 (Rfree = 0.000) for 1073 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1928 (Rfree = 0.000) for 1069 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 1085 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.416 Round 2: 77 peptides, 12 chains. Longest chain 13 peptides. Score 0.496 Round 3: 86 peptides, 11 chains. Longest chain 21 peptides. Score 0.612 Round 4: 85 peptides, 12 chains. Longest chain 11 peptides. Score 0.568 Round 5: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.585 Taking the results from Round 3 Chains 11, Residues 75, Estimated correctness of the model 32.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2408 restraints for refining 1091 atoms. 2119 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2101 (Rfree = 0.000) for 1091 atoms. Found 3 (6 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.1916 (Rfree = 0.000) for 1090 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1874 (Rfree = 0.000) for 1087 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1835 (Rfree = 0.000) for 1083 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1836 (Rfree = 0.000) for 1079 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 1102 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 11 peptides. Score 0.361 Round 2: 64 peptides, 9 chains. Longest chain 20 peptides. Score 0.498 Round 3: 65 peptides, 10 chains. Longest chain 10 peptides. Score 0.464 Round 4: 71 peptides, 9 chains. Longest chain 25 peptides. Score 0.563 Round 5: 64 peptides, 10 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 16.1 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2265 reflections ( 99.52 % complete ) and 2261 restraints for refining 1091 atoms. 1942 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2122 (Rfree = 0.000) for 1091 atoms. Found 6 (6 requested) and removed 12 (4 requested) atoms. Cycle 42: After refmac, R = 0.1850 (Rfree = 0.000) for 1082 atoms. Found 2 (6 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2177 (Rfree = 0.000) for 1080 atoms. Found 4 (6 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 1077 atoms. Found 1 (6 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1637 (Rfree = 0.000) for 1072 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1100 seeds are put forward Round 1: 66 peptides, 11 chains. Longest chain 14 peptides. Score 0.429 Round 2: 69 peptides, 10 chains. Longest chain 15 peptides. Score 0.503 Round 3: 77 peptides, 11 chains. Longest chain 15 peptides. Score 0.537 Round 4: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.505 Round 5: 80 peptides, 10 chains. Longest chain 15 peptides. Score 0.600 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 70, Estimated correctness of the model 28.7 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2hhz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2265 reflections ( 99.52 % complete ) and 2269 restraints for refining 1091 atoms. 1962 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2065 (Rfree = 0.000) for 1091 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1980 (Rfree = 0.000) for 1086 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1889 (Rfree = 0.000) for 1082 atoms. Found 0 (6 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.1918 (Rfree = 0.000) for 1078 atoms. Found 0 (6 requested) and removed 2 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:33 GMT 2018 Job finished. TimeTaking 24.68 Used memory is bytes: 19152632