null Sun 23 Dec 22:22:59 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 1vjf-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-4.0-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/1vjf-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-4.0-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 22:23:08 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/1vjf-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-4.0-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 112 and 0 Target number of residues in the AU: 112 Target solvent content: 0.6146 Checking the provided sequence file Detected sequence length: 180 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 180 Adjusted target solvent content: 0.38 Input MTZ file: 1vjf-4.0-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: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 target number of atoms Had to go as low as 0.60 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: 46.944 4.001 Wilson plot Bfac: 57.56 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1554 reflections ( 99.62 % complete ) and 0 restraints for refining 1599 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2857 (Rfree = 0.000) for 1599 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 1627 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 6 peptides. Score 0.213 Round 2: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.426 Round 3: 84 peptides, 15 chains. Longest chain 11 peptides. Score 0.426 Round 4: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.457 Round 5: 84 peptides, 13 chains. Longest chain 10 peptides. Score 0.505 Taking the results from Round 5 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 3175 restraints for refining 1300 atoms. 2904 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3067 (Rfree = 0.000) for 1300 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.2934 (Rfree = 0.000) for 1266 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2888 (Rfree = 0.000) for 1246 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.2390 (Rfree = 0.000) for 1232 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2752 (Rfree = 0.000) for 1226 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 1262 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.263 Round 2: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.435 Round 3: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.502 Round 4: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.431 Round 5: 71 peptides, 10 chains. Longest chain 21 peptides. Score 0.507 Taking the results from Round 5 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2704 restraints for refining 1148 atoms. 2470 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2827 (Rfree = 0.000) for 1148 atoms. Found 5 (5 requested) and removed 27 (2 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 1110 atoms. Found 4 (5 requested) and removed 20 (2 requested) atoms. Cycle 8: After refmac, R = 0.2040 (Rfree = 0.000) for 1089 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. Cycle 9: After refmac, R = 0.2219 (Rfree = 0.000) for 1076 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 1070 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 1094 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 5 peptides. Score 0.220 Round 2: 64 peptides, 12 chains. Longest chain 11 peptides. Score 0.352 Round 3: 65 peptides, 11 chains. Longest chain 11 peptides. Score 0.407 Round 4: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.284 Round 5: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 3 Chains 12, Residues 54, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2299 restraints for refining 1054 atoms. 2060 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2521 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2950 (Rfree = 0.000) for 1043 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 13: After refmac, R = 0.2494 (Rfree = 0.000) for 1028 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2563 (Rfree = 0.000) for 1020 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2342 (Rfree = 0.000) for 1015 atoms. Found 1 (4 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 1055 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 5 peptides. Score 0.253 Round 2: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.284 Round 3: 60 peptides, 10 chains. Longest chain 12 peptides. Score 0.400 Round 4: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.339 Round 5: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.371 Taking the results from Round 3 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2285 restraints for refining 988 atoms. 2095 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2504 (Rfree = 0.000) for 988 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 17: After refmac, R = 0.2230 (Rfree = 0.000) for 980 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2082 (Rfree = 0.000) for 976 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2087 (Rfree = 0.000) for 969 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2358 (Rfree = 0.000) for 965 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.229 Round 2: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.368 Round 3: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.373 Round 4: 60 peptides, 9 chains. Longest chain 18 peptides. Score 0.445 Round 5: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.387 Taking the results from Round 4 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2217 restraints for refining 990 atoms. 2022 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2509 (Rfree = 0.000) for 990 atoms. Found 3 (4 requested) and removed 8 (2 requested) atoms. Cycle 22: After refmac, R = 0.2263 (Rfree = 0.000) for 980 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2036 (Rfree = 0.000) for 977 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1970 (Rfree = 0.000) for 974 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1964 (Rfree = 0.000) for 972 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 1000 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 11 peptides. Score 0.291 Round 2: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.282 Round 3: 45 peptides, 7 chains. Longest chain 10 peptides. Score 0.382 Round 4: 44 peptides, 8 chains. Longest chain 11 peptides. Score 0.321 Round 5: 46 peptides, 7 chains. Longest chain 12 peptides. Score 0.393 Taking the results from Round 5 Chains 7, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2394 restraints for refining 1020 atoms. 2245 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2256 (Rfree = 0.000) for 1020 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.2319 (Rfree = 0.000) for 1017 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. Cycle 28: After refmac, R = 0.2199 (Rfree = 0.000) for 1009 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. Cycle 29: After refmac, R = 0.2068 (Rfree = 0.000) for 1003 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.2535 (Rfree = 0.000) for 998 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 1034 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.243 Round 2: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.314 Round 3: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.371 Round 4: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.384 Round 5: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 4 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2221 restraints for refining 1030 atoms. 1997 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2300 (Rfree = 0.000) for 1030 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.2237 (Rfree = 0.000) for 1017 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2163 (Rfree = 0.000) for 1010 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 1007 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 1005 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 4.07 Search for helices and strands: 0 residues in 0 chains, 1049 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.206 Round 2: 59 peptides, 12 chains. Longest chain 9 peptides. Score 0.297 Round 3: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.331 Round 4: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.381 Round 5: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.363 Taking the results from Round 4 Chains 13, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2337 restraints for refining 1032 atoms. 2118 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2368 (Rfree = 0.000) for 1032 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.2343 (Rfree = 0.000) for 1027 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.2247 (Rfree = 0.000) for 1017 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2413 (Rfree = 0.000) for 1008 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2331 (Rfree = 0.000) for 1009 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 1043 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 6 peptides. Score 0.208 Round 2: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.220 Round 3: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.282 Round 4: 45 peptides, 8 chains. Longest chain 11 peptides. Score 0.332 Round 5: 48 peptides, 7 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 5 Chains 7, Residues 41, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1554 reflections ( 99.62 % complete ) and 2304 restraints for refining 1046 atoms. 2115 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2233 (Rfree = 0.000) for 1046 atoms. Found 3 (4 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.2072 (Rfree = 0.000) for 1037 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.1916 (Rfree = 0.000) for 1031 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.1953 (Rfree = 0.000) for 1025 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2451 (Rfree = 0.000) for 1021 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 1062 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.180 Round 2: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.347 Round 3: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.277 Round 4: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.390 Round 5: 56 peptides, 10 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjf-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1554 reflections ( 99.62 % complete ) and 2399 restraints for refining 1048 atoms. 2213 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2757 (Rfree = 0.000) for 1048 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3002 (Rfree = 0.000) for 1041 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2341 (Rfree = 0.000) for 1033 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2388 (Rfree = 0.000) for 1029 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:08 GMT 2018 Job finished. TimeTaking 24.15 Used memory is bytes: 13380344