null Sun 23 Dec 22:22:49 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 2okf-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.6-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/2okf-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.6-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 22:22:59 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/2okf-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.6-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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6447 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-3.6-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.6-parrot-hancs.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 3.601 Wilson plot Bfac: 74.38 3386 reflections ( 99.53 % complete ) and 0 restraints for refining 2473 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3412 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 2505 seeds are put forward NCS extension: 0 residues added, 2505 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.293 Round 2: 144 peptides, 26 chains. Longest chain 11 peptides. Score 0.397 Round 3: 137 peptides, 23 chains. Longest chain 11 peptides. Score 0.427 Round 4: 149 peptides, 22 chains. Longest chain 14 peptides. Score 0.507 Round 5: 156 peptides, 25 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 4 Chains 22, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4618 restraints for refining 2030 atoms. 4132 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2367 (Rfree = 0.000) for 2030 atoms. Found 6 (13 requested) and removed 27 (6 requested) atoms. Cycle 2: After refmac, R = 0.2327 (Rfree = 0.000) for 1988 atoms. Found 5 (12 requested) and removed 22 (6 requested) atoms. Cycle 3: After refmac, R = 0.2354 (Rfree = 0.000) for 1960 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.2144 (Rfree = 0.000) for 1952 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.2091 (Rfree = 0.000) for 1941 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.50 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2013 seeds are put forward Round 1: 137 peptides, 24 chains. Longest chain 13 peptides. Score 0.405 Round 2: 141 peptides, 21 chains. Longest chain 13 peptides. Score 0.490 Round 3: 129 peptides, 20 chains. Longest chain 12 peptides. Score 0.453 Round 4: 148 peptides, 21 chains. Longest chain 13 peptides. Score 0.522 Round 5: 153 peptides, 20 chains. Longest chain 17 peptides. Score 0.563 Taking the results from Round 5 Chains 20, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4635 restraints for refining 2018 atoms. 4123 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2220 (Rfree = 0.000) for 2018 atoms. Found 3 (12 requested) and removed 23 (6 requested) atoms. Cycle 7: After refmac, R = 0.2165 (Rfree = 0.000) for 1983 atoms. Found 3 (12 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2104 (Rfree = 0.000) for 1971 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2095 (Rfree = 0.000) for 1961 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 1956 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.47 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 2046 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 15 peptides. Score 0.399 Round 2: 151 peptides, 23 chains. Longest chain 16 peptides. Score 0.496 Round 3: 155 peptides, 23 chains. Longest chain 23 peptides. Score 0.514 Round 4: 165 peptides, 23 chains. Longest chain 19 peptides. Score 0.558 Round 5: 152 peptides, 21 chains. Longest chain 23 peptides. Score 0.540 Taking the results from Round 4 Chains 24, Residues 142, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4443 restraints for refining 2031 atoms. 3863 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2275 (Rfree = 0.000) for 2031 atoms. Found 5 (13 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.2134 (Rfree = 0.000) for 2009 atoms. Found 2 (12 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.2074 (Rfree = 0.000) for 1997 atoms. Found 2 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2008 (Rfree = 0.000) for 1986 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2019 (Rfree = 0.000) for 1977 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 2071 seeds are put forward Round 1: 138 peptides, 24 chains. Longest chain 16 peptides. Score 0.410 Round 2: 153 peptides, 23 chains. Longest chain 17 peptides. Score 0.505 Round 3: 167 peptides, 24 chains. Longest chain 16 peptides. Score 0.547 Round 4: 161 peptides, 22 chains. Longest chain 16 peptides. Score 0.559 Round 5: 154 peptides, 24 chains. Longest chain 12 peptides. Score 0.489 Taking the results from Round 4 Chains 22, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4510 restraints for refining 2029 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2257 (Rfree = 0.000) for 2029 atoms. Found 3 (13 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2115 (Rfree = 0.000) for 2015 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.2189 (Rfree = 0.000) for 2006 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1983 (Rfree = 0.000) for 2001 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 1995 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 0 residues added, 2060 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.328 Round 2: 136 peptides, 22 chains. Longest chain 13 peptides. Score 0.444 Round 3: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.451 Round 4: 156 peptides, 23 chains. Longest chain 18 peptides. Score 0.518 Round 5: 137 peptides, 19 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 4 Chains 23, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4491 restraints for refining 2031 atoms. 3982 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2391 (Rfree = 0.000) for 2031 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2091 (Rfree = 0.000) for 2010 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1896 (Rfree = 0.000) for 2004 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 1993 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.1864 (Rfree = 0.000) for 1984 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2083 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.288 Round 2: 138 peptides, 23 chains. Longest chain 16 peptides. Score 0.432 Round 3: 152 peptides, 25 chains. Longest chain 15 peptides. Score 0.459 Round 4: 149 peptides, 22 chains. Longest chain 13 peptides. Score 0.507 Round 5: 143 peptides, 25 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 4 Chains 22, Residues 127, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4407 restraints for refining 2031 atoms. 3843 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2382 (Rfree = 0.000) for 2031 atoms. Found 4 (13 requested) and removed 18 (6 requested) atoms. Cycle 27: After refmac, R = 0.2058 (Rfree = 0.000) for 2011 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.1950 (Rfree = 0.000) for 2000 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1938 (Rfree = 0.000) for 1994 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1951 (Rfree = 0.000) for 1983 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 2033 seeds are put forward NCS extension: 0 residues added, 2033 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.275 Round 2: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.385 Round 3: 123 peptides, 21 chains. Longest chain 10 peptides. Score 0.399 Round 4: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.332 Round 5: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 3 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4693 restraints for refining 2029 atoms. 4306 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2228 (Rfree = 0.000) for 2029 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.2005 (Rfree = 0.000) for 2019 atoms. Found 0 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1914 (Rfree = 0.000) for 2008 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1941 (Rfree = 0.000) for 2003 atoms. Found 0 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1918 (Rfree = 0.000) for 1994 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.50 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2054 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 9 peptides. Score 0.269 Round 2: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.394 Round 3: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.432 Round 4: 120 peptides, 18 chains. Longest chain 12 peptides. Score 0.452 Round 5: 116 peptides, 18 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 4 Chains 18, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4718 restraints for refining 2031 atoms. 4328 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2121 (Rfree = 0.000) for 2031 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2058 (Rfree = 0.000) for 2023 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 2014 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1808 (Rfree = 0.000) for 2006 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1777 (Rfree = 0.000) for 2002 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.47 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 0 residues added, 2057 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.275 Round 2: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.373 Round 3: 110 peptides, 16 chains. Longest chain 12 peptides. Score 0.446 Round 4: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.346 Round 5: 107 peptides, 17 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 3 Chains 16, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3386 reflections ( 99.53 % complete ) and 4684 restraints for refining 2031 atoms. 4324 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2014 (Rfree = 0.000) for 2031 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1833 (Rfree = 0.000) for 2023 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1795 (Rfree = 0.000) for 2016 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1739 (Rfree = 0.000) for 2010 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1729 (Rfree = 0.000) for 2004 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 2061 seeds are put forward NCS extension: 0 residues added, 2061 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 16 peptides. Score 0.309 Round 2: 105 peptides, 17 chains. Longest chain 16 peptides. Score 0.396 Round 3: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.367 Round 4: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.426 Round 5: 123 peptides, 22 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 97, 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. 3386 reflections ( 99.53 % complete ) and 4730 restraints for refining 2031 atoms. 4360 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1984 (Rfree = 0.000) for 2031 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1835 (Rfree = 0.000) for 2024 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1846 (Rfree = 0.000) for 2018 atoms. Found 0 (12 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.1823 (Rfree = 0.000) for 2017 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:24 GMT 2018 Job finished. TimeTaking 42.57 Used memory is bytes: 13323840