null Mon 24 Dec 01:10:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prv-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prv-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:10:19 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prv-4.0-parrot-mrncs/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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6643 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-4.0-parrot-mrncs.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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 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 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: 44.420 4.000 Wilson plot Bfac: 86.85 2458 reflections ( 97.69 % complete ) and 0 restraints for refining 2703 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3910 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3247 (Rfree = 0.000) for 2703 atoms. Found 5 (12 requested) and removed 110 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.84 Search for helices and strands: 0 residues in 0 chains, 2611 seeds are put forward NCS extension: 0 residues added, 2611 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.213 Round 2: 75 peptides, 17 chains. Longest chain 8 peptides. Score 0.215 Round 3: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.265 Round 4: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.270 Round 5: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.270 Taking the results from Round 5 Chains 19, Residues 73, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 5377 restraints for refining 2211 atoms. 5074 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2469 (Rfree = 0.000) for 2211 atoms. Found 6 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2137 (Rfree = 0.000) for 2187 atoms. Found 3 (10 requested) and removed 17 (5 requested) atoms. Cycle 3: After refmac, R = 0.1841 (Rfree = 0.000) for 2162 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2084 (Rfree = 0.000) for 2150 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.1764 (Rfree = 0.000) for 2135 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 2174 seeds are put forward NCS extension: 0 residues added, 2174 seeds are put forward Round 1: 68 peptides, 16 chains. Longest chain 5 peptides. Score 0.195 Round 2: 81 peptides, 19 chains. Longest chain 5 peptides. Score 0.200 Round 3: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.258 Round 4: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.287 Round 5: 92 peptides, 19 chains. Longest chain 11 peptides. Score 0.270 Taking the results from Round 4 Chains 20, Residues 79, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4616 restraints for refining 2010 atoms. 4300 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2117 (Rfree = 0.000) for 2010 atoms. Found 3 (9 requested) and removed 19 (4 requested) atoms. Cycle 7: After refmac, R = 0.1957 (Rfree = 0.000) for 1982 atoms. Found 3 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.1790 (Rfree = 0.000) for 1969 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.1554 (Rfree = 0.000) for 1959 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.1469 (Rfree = 0.000) for 1954 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.91 Search for helices and strands: 0 residues in 0 chains, 1987 seeds are put forward NCS extension: 0 residues added, 1987 seeds are put forward Round 1: 95 peptides, 23 chains. Longest chain 6 peptides. Score 0.186 Round 2: 102 peptides, 22 chains. Longest chain 7 peptides. Score 0.255 Round 3: 96 peptides, 21 chains. Longest chain 9 peptides. Score 0.243 Round 4: 113 peptides, 23 chains. Longest chain 7 peptides. Score 0.295 Round 5: 115 peptides, 23 chains. Longest chain 10 peptides. Score 0.306 Taking the results from Round 5 Chains 23, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4669 restraints for refining 2038 atoms. 4324 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2107 (Rfree = 0.000) for 2038 atoms. Found 7 (9 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.1906 (Rfree = 0.000) for 2015 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.1663 (Rfree = 0.000) for 2007 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1635 (Rfree = 0.000) for 1995 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2285 (Rfree = 0.000) for 1985 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 0 residues added, 2039 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 6 peptides. Score 0.227 Round 2: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.254 Round 3: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.323 Round 4: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.346 Round 5: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.305 Taking the results from Round 4 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4745 restraints for refining 2055 atoms. 4457 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1679 (Rfree = 0.000) for 2055 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.1550 (Rfree = 0.000) for 2038 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.1553 (Rfree = 0.000) for 2030 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.1485 (Rfree = 0.000) for 2025 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.1455 (Rfree = 0.000) for 2018 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 0 residues added, 2064 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.216 Round 2: 82 peptides, 16 chains. Longest chain 12 peptides. Score 0.287 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.287 Round 4: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.272 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.289 Taking the results from Round 5 Chains 15, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4862 restraints for refining 2064 atoms. 4625 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1711 (Rfree = 0.000) for 2064 atoms. Found 2 (9 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.1544 (Rfree = 0.000) for 2043 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.1541 (Rfree = 0.000) for 2034 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.1444 (Rfree = 0.000) for 2031 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1457 (Rfree = 0.000) for 2025 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 0 residues added, 2050 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 8 peptides. Score 0.214 Round 2: 94 peptides, 19 chains. Longest chain 12 peptides. Score 0.282 Round 3: 93 peptides, 17 chains. Longest chain 12 peptides. Score 0.327 Round 4: 95 peptides, 18 chains. Longest chain 11 peptides. Score 0.313 Round 5: 88 peptides, 17 chains. Longest chain 12 peptides. Score 0.297 Taking the results from Round 3 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4757 restraints for refining 2069 atoms. 4470 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1675 (Rfree = 0.000) for 2069 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 27: After refmac, R = 0.1540 (Rfree = 0.000) for 2060 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1550 (Rfree = 0.000) for 2053 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.1493 (Rfree = 0.000) for 2048 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1485 (Rfree = 0.000) for 2044 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2087 seeds are put forward NCS extension: 0 residues added, 2087 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 7 peptides. Score 0.203 Round 2: 76 peptides, 14 chains. Longest chain 12 peptides. Score 0.303 Round 3: 78 peptides, 14 chains. Longest chain 12 peptides. Score 0.315 Round 4: 81 peptides, 15 chains. Longest chain 14 peptides. Score 0.307 Round 5: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 3 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4821 restraints for refining 2079 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1486 (Rfree = 0.000) for 2079 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.1454 (Rfree = 0.000) for 2073 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1382 (Rfree = 0.000) for 2073 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.1289 (Rfree = 0.000) for 2066 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1363 (Rfree = 0.000) for 2063 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2089 seeds are put forward NCS extension: 0 residues added, 2089 seeds are put forward Round 1: 66 peptides, 16 chains. Longest chain 5 peptides. Score 0.181 Round 2: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.247 Round 3: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.229 Round 4: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.295 Round 5: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.257 Taking the results from Round 4 Chains 15, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 4918 restraints for refining 2098 atoms. 4677 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1496 (Rfree = 0.000) for 2098 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.1428 (Rfree = 0.000) for 2093 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.1399 (Rfree = 0.000) for 2088 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1494 (Rfree = 0.000) for 2080 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1403 (Rfree = 0.000) for 2077 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.93 Search for helices and strands: 0 residues in 0 chains, 2111 seeds are put forward NCS extension: 0 residues added, 2111 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 9 peptides. Score 0.213 Round 2: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.240 Round 3: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.251 Round 4: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.272 Round 5: 55 peptides, 10 chains. Longest chain 7 peptides. Score 0.282 Taking the results from Round 5 Chains 10, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 97.69 % complete ) and 5018 restraints for refining 2122 atoms. 4848 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1512 (Rfree = 0.000) for 2122 atoms. Found 2 (10 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.1434 (Rfree = 0.000) for 2111 atoms. Found 0 (10 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.1402 (Rfree = 0.000) for 2101 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1293 (Rfree = 0.000) for 2094 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1405 (Rfree = 0.000) for 2091 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.95 Search for helices and strands: 0 residues in 0 chains, 2120 seeds are put forward NCS extension: 0 residues added, 2120 seeds are put forward Round 1: 54 peptides, 13 chains. Longest chain 5 peptides. Score 0.182 Round 2: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.235 Round 3: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.228 Round 4: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.220 Round 5: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.219 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 45, 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 2prv-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2458 reflections ( 97.69 % complete ) and 5100 restraints for refining 2099 atoms. 4932 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1540 (Rfree = 0.000) for 2099 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1422 (Rfree = 0.000) for 2090 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1424 (Rfree = 0.000) for 2086 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1362 (Rfree = 0.000) for 2081 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:36:21 GMT 2018 Job finished. TimeTaking 26.1 Used memory is bytes: 19473936