Mon 24 Dec 00:24:55 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 2okf-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.8-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/2okf-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.8-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 00:25:00 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/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.8-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6554 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 280 Adjusted target solvent content: 0.50 Input MTZ file: 2okf-3.8-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2240 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: 27.710 3.804 Wilson plot Bfac: 81.05 2872 reflections ( 99.45 % complete ) and 0 restraints for refining 2498 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3404 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3220 (Rfree = 0.000) for 2498 atoms. Found 9 (13 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 2510 seeds are put forward NCS extension: 0 residues added, 2510 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.262 Round 2: 123 peptides, 22 chains. Longest chain 16 peptides. Score 0.376 Round 3: 152 peptides, 25 chains. Longest chain 16 peptides. Score 0.459 Round 4: 143 peptides, 22 chains. Longest chain 20 peptides. Score 0.478 Round 5: 151 peptides, 24 chains. Longest chain 18 peptides. Score 0.475 Taking the results from Round 4 Chains 22, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4742 restraints for refining 2026 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2477 (Rfree = 0.000) for 2026 atoms. Found 4 (11 requested) and removed 26 (5 requested) atoms. Cycle 2: After refmac, R = 0.2250 (Rfree = 0.000) for 1987 atoms. Found 3 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2161 (Rfree = 0.000) for 1968 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2117 (Rfree = 0.000) for 1961 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 1956 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 2009 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2031 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.356 Round 2: 144 peptides, 25 chains. Longest chain 15 peptides. Score 0.419 Round 3: 140 peptides, 22 chains. Longest chain 13 peptides. Score 0.464 Round 4: 149 peptides, 25 chains. Longest chain 10 peptides. Score 0.444 Round 5: 152 peptides, 22 chains. Longest chain 18 peptides. Score 0.520 Taking the results from Round 5 Chains 22, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4586 restraints for refining 1996 atoms. 4088 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 1996 atoms. Found 3 (10 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 1978 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2227 (Rfree = 0.000) for 1972 atoms. Found 0 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2201 (Rfree = 0.000) for 1963 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 1959 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 2020 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2045 seeds are put forward Round 1: 125 peptides, 23 chains. Longest chain 9 peptides. Score 0.364 Round 2: 133 peptides, 21 chains. Longest chain 17 peptides. Score 0.451 Round 3: 127 peptides, 19 chains. Longest chain 12 peptides. Score 0.465 Round 4: 147 peptides, 19 chains. Longest chain 20 peptides. Score 0.557 Round 5: 141 peptides, 19 chains. Longest chain 26 peptides. Score 0.531 Taking the results from Round 4 Chains 21, Residues 128, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4578 restraints for refining 2026 atoms. 4046 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2444 (Rfree = 0.000) for 2026 atoms. Found 7 (11 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.2226 (Rfree = 0.000) for 2010 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 2001 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2146 (Rfree = 0.000) for 1994 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2133 (Rfree = 0.000) for 1991 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2066 seeds are put forward Round 1: 142 peptides, 24 chains. Longest chain 19 peptides. Score 0.431 Round 2: 160 peptides, 24 chains. Longest chain 21 peptides. Score 0.517 Round 3: 154 peptides, 24 chains. Longest chain 18 peptides. Score 0.489 Round 4: 156 peptides, 24 chains. Longest chain 15 peptides. Score 0.498 Round 5: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 2 Chains 24, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4633 restraints for refining 2025 atoms. 4113 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2286 (Rfree = 0.000) for 2025 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2169 (Rfree = 0.000) for 2010 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2100 (Rfree = 0.000) for 2001 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2080 (Rfree = 0.000) for 1993 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2111 (Rfree = 0.000) for 1988 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 2039 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 2076 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 8 peptides. Score 0.318 Round 2: 146 peptides, 21 chains. Longest chain 16 peptides. Score 0.513 Round 3: 141 peptides, 20 chains. Longest chain 21 peptides. Score 0.510 Round 4: 147 peptides, 19 chains. Longest chain 17 peptides. Score 0.557 Round 5: 145 peptides, 16 chains. Longest chain 22 peptides. Score 0.606 Taking the results from Round 5 Chains 16, Residues 129, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4784 restraints for refining 2026 atoms. 4284 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2335 (Rfree = 0.000) for 2026 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 22: After refmac, R = 0.2077 (Rfree = 0.000) for 2016 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2020 (Rfree = 0.000) for 2010 atoms. Found 1 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.1913 (Rfree = 0.000) for 1998 atoms. Found 0 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1918 (Rfree = 0.000) for 1989 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2077 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.293 Round 2: 124 peptides, 20 chains. Longest chain 19 peptides. Score 0.427 Round 3: 121 peptides, 18 chains. Longest chain 17 peptides. Score 0.457 Round 4: 125 peptides, 18 chains. Longest chain 19 peptides. Score 0.477 Round 5: 127 peptides, 17 chains. Longest chain 20 peptides. Score 0.508 Taking the results from Round 5 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4676 restraints for refining 2026 atoms. 4207 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2111 (Rfree = 0.000) for 2026 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.1959 (Rfree = 0.000) for 2016 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.1933 (Rfree = 0.000) for 2008 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1883 (Rfree = 0.000) for 2002 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1866 (Rfree = 0.000) for 1996 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 2062 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2092 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 8 peptides. Score 0.274 Round 2: 125 peptides, 23 chains. Longest chain 11 peptides. Score 0.364 Round 3: 115 peptides, 19 chains. Longest chain 16 peptides. Score 0.403 Round 4: 117 peptides, 20 chains. Longest chain 15 peptides. Score 0.390 Round 5: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 3 Chains 19, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4847 restraints for refining 2026 atoms. 4482 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1967 (Rfree = 0.000) for 2026 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.1789 (Rfree = 0.000) for 2015 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1658 (Rfree = 0.000) for 2010 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.1630 (Rfree = 0.000) for 2001 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 1994 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2079 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 9 peptides. Score 0.256 Round 2: 115 peptides, 24 chains. Longest chain 10 peptides. Score 0.283 Round 3: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.354 Round 4: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.354 Round 5: 118 peptides, 19 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 5 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4761 restraints for refining 2026 atoms. 4357 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2012 (Rfree = 0.000) for 2026 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2334 (Rfree = 0.000) for 2017 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.1935 (Rfree = 0.000) for 2010 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2040 (Rfree = 0.000) for 2004 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2138 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.64 Search for helices and strands: 0 residues in 0 chains, 2095 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2108 seeds are put forward Round 1: 60 peptides, 14 chains. Longest chain 5 peptides. Score 0.197 Round 2: 87 peptides, 18 chains. Longest chain 9 peptides. Score 0.266 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.313 Round 4: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.300 Round 5: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2872 reflections ( 99.45 % complete ) and 4687 restraints for refining 1996 atoms. 4353 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2470 (Rfree = 0.000) for 1996 atoms. Found 9 (10 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.2202 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.1932 (Rfree = 0.000) for 1979 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.1439 (Rfree = 0.000) for 1980 atoms. Found 2 (10 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.1367 (Rfree = 0.000) for 1970 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2053 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 7 peptides. Score 0.202 Round 2: 86 peptides, 19 chains. Longest chain 8 peptides. Score 0.233 Round 3: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.256 Round 4: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.302 Round 5: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.290 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 65, 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 2okf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2872 reflections ( 99.45 % complete ) and 4992 restraints for refining 2025 atoms. 4747 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 2025 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2012 (Rfree = 0.000) for 2011 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1735 (Rfree = 0.000) for 2003 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1505 (Rfree = 0.000) for 1996 atoms. TimeTaking 31.53