null Sun 23 Dec 22:22:40 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 1vr8-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.8-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/1vr8-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.8-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 22:22:49 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/1vr8-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.8-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 116 and 0 Target number of residues in the AU: 116 Target solvent content: 0.6296 Checking the provided sequence file Detected sequence length: 142 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 142 Adjusted target solvent content: 0.55 Input MTZ file: 1vr8-3.8-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: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1136 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.023 3.801 Wilson plot Bfac: 66.30 1846 reflections ( 99.68 % complete ) and 0 restraints for refining 1264 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3399 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3215 (Rfree = 0.000) for 1264 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.342 Round 2: 83 peptides, 13 chains. Longest chain 14 peptides. Score 0.478 Round 3: 80 peptides, 9 chains. Longest chain 16 peptides. Score 0.595 Round 4: 94 peptides, 12 chains. Longest chain 17 peptides. Score 0.598 Round 5: 88 peptides, 11 chains. Longest chain 16 peptides. Score 0.587 Taking the results from Round 4 Chains 12, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2209 restraints for refining 1026 atoms. 1893 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2690 (Rfree = 0.000) for 1026 atoms. Found 0 (5 requested) and removed 20 (2 requested) atoms. Cycle 2: After refmac, R = 0.2541 (Rfree = 0.000) for 988 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 3: After refmac, R = 0.2524 (Rfree = 0.000) for 985 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2598 (Rfree = 0.000) for 977 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2555 (Rfree = 0.000) for 969 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 1002 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.345 Round 2: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.458 Round 3: 82 peptides, 10 chains. Longest chain 16 peptides. Score 0.576 Round 4: 80 peptides, 12 chains. Longest chain 14 peptides. Score 0.490 Round 5: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.469 Taking the results from Round 3 Chains 10, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2297 restraints for refining 1026 atoms. 2019 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2540 (Rfree = 0.000) for 1026 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 7: After refmac, R = 0.2749 (Rfree = 0.000) for 1011 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. Cycle 8: After refmac, R = 0.2272 (Rfree = 0.000) for 994 atoms. Found 1 (5 requested) and removed 8 (2 requested) atoms. Cycle 9: After refmac, R = 0.2198 (Rfree = 0.000) for 983 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 980 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 1021 seeds are put forward Round 1: 80 peptides, 11 chains. Longest chain 20 peptides. Score 0.526 Round 2: 78 peptides, 11 chains. Longest chain 11 peptides. Score 0.510 Round 3: 74 peptides, 9 chains. Longest chain 13 peptides. Score 0.550 Round 4: 85 peptides, 9 chains. Longest chain 23 peptides. Score 0.630 Round 5: 82 peptides, 10 chains. Longest chain 14 peptides. Score 0.576 Taking the results from Round 4 Chains 9, Residues 76, Estimated correctness of the model 12.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2277 restraints for refining 1020 atoms. 1982 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2379 (Rfree = 0.000) for 1020 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 12: After refmac, R = 0.2769 (Rfree = 0.000) for 1008 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.2293 (Rfree = 0.000) for 999 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 983 atoms. Found 1 (5 requested) and removed 9 (2 requested) atoms. Cycle 15: After refmac, R = 0.2188 (Rfree = 0.000) for 973 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 65 peptides, 10 chains. Longest chain 16 peptides. Score 0.435 Round 2: 71 peptides, 9 chains. Longest chain 16 peptides. Score 0.526 Round 3: 75 peptides, 9 chains. Longest chain 16 peptides. Score 0.558 Round 4: 71 peptides, 9 chains. Longest chain 17 peptides. Score 0.526 Round 5: 75 peptides, 9 chains. Longest chain 18 peptides. Score 0.558 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2356 restraints for refining 1023 atoms. 2101 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2662 (Rfree = 0.000) for 1023 atoms. Found 2 (5 requested) and removed 49 (2 requested) atoms. Cycle 17: After refmac, R = 0.2789 (Rfree = 0.000) for 969 atoms. Found 3 (5 requested) and removed 21 (2 requested) atoms. Cycle 18: After refmac, R = 0.2786 (Rfree = 0.000) for 951 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 19: After refmac, R = 0.2793 (Rfree = 0.000) for 943 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 20: After refmac, R = 0.2372 (Rfree = 0.000) for 937 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 981 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.324 Round 2: 68 peptides, 10 chains. Longest chain 21 peptides. Score 0.462 Round 3: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.391 Round 4: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.381 Round 5: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.422 Taking the results from Round 2 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2251 restraints for refining 982 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 982 atoms. Found 2 (5 requested) and removed 22 (2 requested) atoms. Cycle 22: After refmac, R = 0.2311 (Rfree = 0.000) for 958 atoms. Found 5 (5 requested) and removed 23 (2 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 938 atoms. Found 1 (5 requested) and removed 9 (2 requested) atoms. Cycle 24: After refmac, R = 0.2227 (Rfree = 0.000) for 927 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 25: After refmac, R = 0.2423 (Rfree = 0.000) for 923 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 966 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.277 Round 2: 70 peptides, 12 chains. Longest chain 14 peptides. Score 0.400 Round 3: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.462 Round 4: 61 peptides, 10 chains. Longest chain 9 peptides. Score 0.397 Round 5: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.416 Taking the results from Round 3 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2281 restraints for refining 988 atoms. 2059 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2601 (Rfree = 0.000) for 988 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. Cycle 27: After refmac, R = 0.2691 (Rfree = 0.000) for 978 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 28: After refmac, R = 0.2510 (Rfree = 0.000) for 974 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 29: After refmac, R = 0.2091 (Rfree = 0.000) for 971 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2458 (Rfree = 0.000) for 969 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.342 Round 2: 74 peptides, 12 chains. Longest chain 15 peptides. Score 0.437 Round 3: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.452 Round 4: 82 peptides, 12 chains. Longest chain 20 peptides. Score 0.506 Round 5: 88 peptides, 12 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 5 Chains 12, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2259 restraints for refining 1027 atoms. 1967 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2672 (Rfree = 0.000) for 1027 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. Cycle 32: After refmac, R = 0.2327 (Rfree = 0.000) for 1003 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.2276 (Rfree = 0.000) for 990 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2368 (Rfree = 0.000) for 985 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 35: After refmac, R = 0.2607 (Rfree = 0.000) for 973 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 1027 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 12 peptides. Score 0.281 Round 2: 63 peptides, 12 chains. Longest chain 12 peptides. Score 0.331 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.334 Round 4: 63 peptides, 9 chains. Longest chain 21 peptides. Score 0.458 Round 5: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.354 Taking the results from Round 4 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2416 restraints for refining 1027 atoms. 2209 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2376 (Rfree = 0.000) for 1027 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 37: After refmac, R = 0.2175 (Rfree = 0.000) for 1019 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.2065 (Rfree = 0.000) for 1016 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2001 (Rfree = 0.000) for 1010 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2045 (Rfree = 0.000) for 1008 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 1037 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 8 peptides. Score 0.256 Round 2: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.397 Round 3: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.354 Round 4: 69 peptides, 12 chains. Longest chain 14 peptides. Score 0.391 Round 5: 78 peptides, 13 chains. Longest chain 9 peptides. Score 0.434 Taking the results from Round 5 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1846 reflections ( 99.68 % complete ) and 2347 restraints for refining 1027 atoms. 2100 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2447 (Rfree = 0.000) for 1027 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 42: After refmac, R = 0.2386 (Rfree = 0.000) for 1017 atoms. Found 2 (5 requested) and removed 10 (2 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 1007 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2276 (Rfree = 0.000) for 1004 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.2199 (Rfree = 0.000) for 997 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 1046 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.292 Round 2: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.449 Round 3: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.409 Round 4: 76 peptides, 12 chains. Longest chain 14 peptides. Score 0.455 Round 5: 67 peptides, 11 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 64, 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 1vr8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1846 reflections ( 99.68 % complete ) and 2277 restraints for refining 1027 atoms. 2033 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2293 (Rfree = 0.000) for 1027 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2209 (Rfree = 0.000) for 1016 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2078 (Rfree = 0.000) for 1008 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2029 (Rfree = 0.000) for 1006 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:20 GMT 2018 Job finished. TimeTaking 24.66 Used memory is bytes: 18994944