null Sun 23 Dec 22:22:42 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 1vr8-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-4.0-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/1vr8-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-4.0-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 22:22:56 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/1vr8-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-4.0-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 113 and 0 Target number of residues in the AU: 113 Target solvent content: 0.6391 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: 1vr8-4.0-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: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-4.0-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 4.000 Wilson plot Bfac: 71.15 1598 reflections ( 99.63 % complete ) and 0 restraints for refining 1262 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3442 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2763 (Rfree = 0.000) for 1262 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 14 peptides. Score 0.420 Round 2: 92 peptides, 12 chains. Longest chain 16 peptides. Score 0.584 Round 3: 92 peptides, 10 chains. Longest chain 16 peptides. Score 0.646 Round 4: 93 peptides, 11 chains. Longest chain 14 peptides. Score 0.622 Round 5: 96 peptides, 11 chains. Longest chain 18 peptides. Score 0.642 Taking the results from Round 3 Chains 10, Residues 82, Estimated correctness of the model 5.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2277 restraints for refining 1025 atoms. 1959 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2516 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 2: After refmac, R = 0.2523 (Rfree = 0.000) for 998 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 3: After refmac, R = 0.2393 (Rfree = 0.000) for 978 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 4: After refmac, R = 0.2405 (Rfree = 0.000) for 966 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 5: After refmac, R = 0.2227 (Rfree = 0.000) for 955 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.42 Search for helices and strands: 0 residues in 0 chains, 978 seeds are put forward Round 1: 71 peptides, 11 chains. Longest chain 18 peptides. Score 0.449 Round 2: 89 peptides, 14 chains. Longest chain 15 peptides. Score 0.492 Round 3: 87 peptides, 12 chains. Longest chain 14 peptides. Score 0.546 Round 4: 83 peptides, 10 chains. Longest chain 19 peptides. Score 0.584 Round 5: 86 peptides, 11 chains. Longest chain 17 peptides. Score 0.572 Taking the results from Round 4 Chains 11, Residues 73, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2265 restraints for refining 1025 atoms. 1940 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2901 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 7: After refmac, R = 0.2346 (Rfree = 0.000) for 993 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 978 atoms. Found 1 (4 requested) and removed 11 (2 requested) atoms. Cycle 9: After refmac, R = 0.2099 (Rfree = 0.000) for 966 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2049 (Rfree = 0.000) for 962 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 1006 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.391 Round 2: 72 peptides, 11 chains. Longest chain 9 peptides. Score 0.458 Round 3: 76 peptides, 12 chains. Longest chain 15 peptides. Score 0.455 Round 4: 74 peptides, 10 chains. Longest chain 13 peptides. Score 0.514 Round 5: 79 peptides, 10 chains. Longest chain 13 peptides. Score 0.554 Taking the results from Round 5 Chains 10, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2462 restraints for refining 1026 atoms. 2196 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2454 (Rfree = 0.000) for 1026 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.2350 (Rfree = 0.000) for 1005 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2072 (Rfree = 0.000) for 996 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 14: After refmac, R = 0.2020 (Rfree = 0.000) for 990 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.1816 (Rfree = 0.000) for 987 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 9 peptides. Score 0.313 Round 2: 73 peptides, 13 chains. Longest chain 12 peptides. Score 0.388 Round 3: 68 peptides, 13 chains. Longest chain 10 peptides. Score 0.339 Round 4: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.422 Round 5: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 4 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2443 restraints for refining 1024 atoms. 2226 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2231 (Rfree = 0.000) for 1024 atoms. Found 3 (4 requested) and removed 11 (2 requested) atoms. Cycle 17: After refmac, R = 0.1955 (Rfree = 0.000) for 1013 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.1900 (Rfree = 0.000) for 1010 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.1825 (Rfree = 0.000) for 1005 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 1002 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 1030 seeds are put forward Round 1: 58 peptides, 10 chains. Longest chain 12 peptides. Score 0.368 Round 2: 71 peptides, 11 chains. Longest chain 13 peptides. Score 0.449 Round 3: 69 peptides, 9 chains. Longest chain 13 peptides. Score 0.510 Round 4: 66 peptides, 9 chains. Longest chain 15 peptides. Score 0.484 Round 5: 71 peptides, 8 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 5 Chains 8, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2379 restraints for refining 1026 atoms. 2135 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2113 (Rfree = 0.000) for 1026 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 22: After refmac, R = 0.2145 (Rfree = 0.000) for 1015 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.1984 (Rfree = 0.000) for 1008 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1968 (Rfree = 0.000) for 1001 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.1889 (Rfree = 0.000) for 996 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 1030 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.269 Round 2: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.327 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.394 Round 4: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.419 Round 5: 69 peptides, 10 chains. Longest chain 10 peptides. Score 0.471 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2420 restraints for refining 1026 atoms. 2194 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2205 (Rfree = 0.000) for 1026 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.2102 (Rfree = 0.000) for 1016 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 1015 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1865 (Rfree = 0.000) for 1013 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.1763 (Rfree = 0.000) for 1009 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 1054 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.316 Round 2: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.271 Round 3: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.295 Round 4: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.358 Round 5: 60 peptides, 13 chains. Longest chain 6 peptides. Score 0.256 Taking the results from Round 4 Chains 10, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2563 restraints for refining 1026 atoms. 2385 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2088 (Rfree = 0.000) for 1026 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.1967 (Rfree = 0.000) for 1022 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.1838 (Rfree = 0.000) for 1022 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1755 (Rfree = 0.000) for 1017 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1766 (Rfree = 0.000) for 1012 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 1031 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.191 Round 2: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.226 Round 3: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.331 Round 4: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.292 Round 5: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 3 Chains 12, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2546 restraints for refining 1026 atoms. 2354 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2891 (Rfree = 0.000) for 1026 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.2838 (Rfree = 0.000) for 1015 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 38: After refmac, R = 0.2873 (Rfree = 0.000) for 999 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.3359 (Rfree = 0.000) for 993 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 40: After refmac, R = 0.2896 (Rfree = 0.000) for 971 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 1021 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.180 Round 2: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.204 Round 3: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.250 Round 4: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.368 Round 5: 49 peptides, 9 chains. Longest chain 11 peptides. Score 0.320 Taking the results from Round 4 Chains 10, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1598 reflections ( 99.63 % complete ) and 2243 restraints for refining 962 atoms. 2061 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2972 (Rfree = 0.000) for 962 atoms. Found 4 (4 requested) and removed 36 (2 requested) atoms. Cycle 42: After refmac, R = 0.2854 (Rfree = 0.000) for 919 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 43: After refmac, R = 0.2460 (Rfree = 0.000) for 908 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2220 (Rfree = 0.000) for 906 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2188 (Rfree = 0.000) for 901 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 922 seeds are put forward Round 1: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.243 Round 2: 41 peptides, 7 chains. Longest chain 8 peptides. Score 0.328 Round 3: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.330 Round 4: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.341 Round 5: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.316 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 42, 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 1vr8-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1598 reflections ( 99.63 % complete ) and 2140 restraints for refining 909 atoms. 1981 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2402 (Rfree = 0.000) for 909 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2368 (Rfree = 0.000) for 901 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2119 (Rfree = 0.000) for 896 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2021 (Rfree = 0.000) for 894 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:23 GMT 2018 Job finished. TimeTaking 55.69 Used memory is bytes: 15540760