null Sun 23 Dec 22:22:43 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 2o1q-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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/2o1q-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 22:22:52 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/2o1q-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 174 and 0 Target number of residues in the AU: 174 Target solvent content: 0.6315 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 56.142 3.600 Wilson plot Bfac: 67.20 3329 reflections ( 99.70 % complete ) and 0 restraints for refining 2583 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3311 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3620 (Rfree = 0.000) for 2583 atoms. Found 16 (16 requested) and removed 50 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.74 Search for helices and strands: 0 residues in 0 chains, 2577 seeds are put forward NCS extension: 0 residues added, 2577 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 8 peptides. Score 0.227 Round 2: 116 peptides, 23 chains. Longest chain 8 peptides. Score 0.334 Round 3: 132 peptides, 24 chains. Longest chain 15 peptides. Score 0.408 Round 4: 124 peptides, 18 chains. Longest chain 18 peptides. Score 0.511 Round 5: 129 peptides, 23 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 4 Chains 18, Residues 106, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4584 restraints for refining 2103 atoms. 4098 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.2226 (Rfree = 0.000) for 2070 atoms. Found 2 (13 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2278 (Rfree = 0.000) for 2050 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.1778 (Rfree = 0.000) for 2045 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.1915 (Rfree = 0.000) for 2041 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2091 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 2117 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 10 peptides. Score 0.320 Round 2: 156 peptides, 28 chains. Longest chain 9 peptides. Score 0.450 Round 3: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.488 Round 4: 145 peptides, 23 chains. Longest chain 16 peptides. Score 0.506 Round 5: 142 peptides, 21 chains. Longest chain 16 peptides. Score 0.536 Taking the results from Round 5 Chains 22, Residues 121, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4847 restraints for refining 2103 atoms. 4351 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 2085 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2161 (Rfree = 0.000) for 2073 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.1996 (Rfree = 0.000) for 2069 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.1950 (Rfree = 0.000) for 2064 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2113 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2124 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 6 peptides. Score 0.251 Round 2: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.413 Round 3: 125 peptides, 22 chains. Longest chain 10 peptides. Score 0.417 Round 4: 140 peptides, 19 chains. Longest chain 13 peptides. Score 0.570 Round 5: 143 peptides, 19 chains. Longest chain 29 peptides. Score 0.585 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 8.7 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4523 restraints for refining 2103 atoms. 3966 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2212 (Rfree = 0.000) for 2103 atoms. Found 9 (13 requested) and removed 15 (6 requested) atoms. Cycle 12: After refmac, R = 0.2149 (Rfree = 0.000) for 2074 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.1964 (Rfree = 0.000) for 2067 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 14: After refmac, R = 0.2012 (Rfree = 0.000) for 2057 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1869 (Rfree = 0.000) for 2053 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 2137 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 10 peptides. Score 0.319 Round 2: 119 peptides, 20 chains. Longest chain 19 peptides. Score 0.432 Round 3: 111 peptides, 18 chains. Longest chain 16 peptides. Score 0.436 Round 4: 127 peptides, 20 chains. Longest chain 11 peptides. Score 0.479 Round 5: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.475 Taking the results from Round 4 Chains 20, Residues 107, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4502 restraints for refining 2103 atoms. 4050 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2121 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.1824 (Rfree = 0.000) for 2078 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.1783 (Rfree = 0.000) for 2069 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1712 (Rfree = 0.000) for 2066 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1447 (Rfree = 0.000) for 2066 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 2114 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 2116 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 9 peptides. Score 0.295 Round 2: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Round 3: 139 peptides, 22 chains. Longest chain 11 peptides. Score 0.497 Round 4: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.473 Round 5: 144 peptides, 20 chains. Longest chain 13 peptides. Score 0.568 Taking the results from Round 5 Chains 20, Residues 124, Estimated correctness of the model 1.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4681 restraints for refining 2103 atoms. 4191 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2375 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2049 (Rfree = 0.000) for 2086 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.1954 (Rfree = 0.000) for 2082 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2095 (Rfree = 0.000) for 2082 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1966 (Rfree = 0.000) for 2087 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 2152 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2170 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.312 Round 2: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.410 Round 3: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.384 Round 4: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.400 Round 5: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 5 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4840 restraints for refining 2083 atoms. 4466 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2388 (Rfree = 0.000) for 2083 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2270 (Rfree = 0.000) for 2071 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 28: After refmac, R = 0.2114 (Rfree = 0.000) for 2062 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2169 (Rfree = 0.000) for 2060 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1494 (Rfree = 0.000) for 2058 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 2098 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2116 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.273 Round 2: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.354 Round 3: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.399 Round 4: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.376 Round 5: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 3 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4642 restraints for refining 1990 atoms. 4312 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2352 (Rfree = 0.000) for 1990 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2016 (Rfree = 0.000) for 1982 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2192 (Rfree = 0.000) for 1978 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2061 (Rfree = 0.000) for 1973 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2047 (Rfree = 0.000) for 1971 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2028 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 7 peptides. Score 0.235 Round 2: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.328 Round 3: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.328 Round 4: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.367 Round 5: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4313 restraints for refining 1944 atoms. 3980 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 1935 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2086 (Rfree = 0.000) for 1928 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.1972 (Rfree = 0.000) for 1922 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1995 (Rfree = 0.000) for 1922 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward NCS extension: 0 residues added, 1958 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 7 peptides. Score 0.218 Round 2: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.312 Round 3: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.307 Round 4: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.349 Round 5: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 4 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4085 restraints for refining 1848 atoms. 3814 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3407 (Rfree = 0.000) for 1848 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 42: After refmac, R = 0.2138 (Rfree = 0.000) for 1828 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2163 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1641 (Rfree = 0.000) for 1829 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1876 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 1881 seeds are put forward NCS extension: 0 residues added, 1881 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.206 Round 2: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.279 Round 3: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.295 Round 4: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.296 Round 5: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 63, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (63 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3329 reflections ( 99.70 % complete ) and 3789 restraints for refining 1767 atoms. 3520 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2123 (Rfree = 0.000) for 1767 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2037 (Rfree = 0.000) for 1757 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2074 (Rfree = 0.000) for 1749 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1569 (Rfree = 0.000) for 1737 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:52 GMT 2018 Job finished. TimeTaking 34.16 Used memory is bytes: 6745608