Mon 24 Dec 00:24:12 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 2o1q-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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/2o1q-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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 00:24:17 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/2o1q-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.6-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 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-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.6-parrot-mrncs.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 2564 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3273 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3365 (Rfree = 0.000) for 2564 atoms. Found 16 (16 requested) and removed 46 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2561 seeds are put forward NCS extension: 0 residues added, 2561 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 13 peptides. Score 0.333 Round 2: 134 peptides, 23 chains. Longest chain 15 peptides. Score 0.445 Round 3: 151 peptides, 23 chains. Longest chain 12 peptides. Score 0.538 Round 4: 159 peptides, 22 chains. Longest chain 14 peptides. Score 0.598 Round 5: 143 peptides, 21 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 4 Chains 23, Residues 137, Estimated correctness of the model 13.9 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4567 restraints for refining 2103 atoms. 3969 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2717 (Rfree = 0.000) for 2103 atoms. Found 12 (13 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.2407 (Rfree = 0.000) for 2055 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2325 (Rfree = 0.000) for 2041 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2134 (Rfree = 0.000) for 2036 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2264 (Rfree = 0.000) for 2025 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.95 Search for helices and strands: 0 residues in 0 chains, 2080 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2094 seeds are put forward Round 1: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.367 Round 2: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.439 Round 3: 147 peptides, 21 chains. Longest chain 15 peptides. Score 0.561 Round 4: 141 peptides, 22 chains. Longest chain 14 peptides. Score 0.508 Round 5: 143 peptides, 22 chains. Longest chain 15 peptides. Score 0.519 Taking the results from Round 3 Chains 23, Residues 126, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4319 restraints for refining 2022 atoms. 3767 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2296 (Rfree = 0.000) for 2022 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.1989 (Rfree = 0.000) for 1996 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.1871 (Rfree = 0.000) for 1984 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.1882 (Rfree = 0.000) for 1970 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.1949 (Rfree = 0.000) for 1960 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 1993 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2016 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 12 peptides. Score 0.360 Round 2: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.459 Round 3: 151 peptides, 24 chains. Longest chain 14 peptides. Score 0.515 Round 4: 152 peptides, 22 chains. Longest chain 16 peptides. Score 0.564 Round 5: 155 peptides, 26 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 4 Chains 23, Residues 130, Estimated correctness of the model 0.1 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4231 restraints for refining 2024 atoms. 3651 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2335 (Rfree = 0.000) for 2024 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2118 (Rfree = 0.000) for 2003 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2007 (Rfree = 0.000) for 1992 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1900 (Rfree = 0.000) for 1991 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1859 (Rfree = 0.000) for 1984 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2038 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.296 Round 2: 133 peptides, 22 chains. Longest chain 10 peptides. Score 0.464 Round 3: 148 peptides, 23 chains. Longest chain 11 peptides. Score 0.522 Round 4: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.521 Round 5: 145 peptides, 22 chains. Longest chain 13 peptides. Score 0.529 Taking the results from Round 5 Chains 22, Residues 123, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4471 restraints for refining 2076 atoms. 3923 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2673 (Rfree = 0.000) for 2076 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 17: After refmac, R = 0.2408 (Rfree = 0.000) for 2045 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.2359 (Rfree = 0.000) for 2020 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.1825 (Rfree = 0.000) for 2007 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1731 (Rfree = 0.000) for 2002 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2056 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 7 peptides. Score 0.313 Round 2: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.374 Round 3: 136 peptides, 21 chains. Longest chain 14 peptides. Score 0.504 Round 4: 133 peptides, 21 chains. Longest chain 10 peptides. Score 0.488 Round 5: 138 peptides, 21 chains. Longest chain 14 peptides. Score 0.515 Taking the results from Round 5 Chains 23, Residues 117, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4674 restraints for refining 2075 atoms. 4200 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2373 (Rfree = 0.000) for 2075 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2156 (Rfree = 0.000) for 2059 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2022 (Rfree = 0.000) for 2053 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 24: After refmac, R = 0.1941 (Rfree = 0.000) for 2048 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1792 (Rfree = 0.000) for 2043 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 2076 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2088 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 11 peptides. Score 0.315 Round 2: 125 peptides, 22 chains. Longest chain 9 peptides. Score 0.417 Round 3: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.439 Round 4: 131 peptides, 22 chains. Longest chain 11 peptides. Score 0.452 Round 5: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.495 Taking the results from Round 5 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4874 restraints for refining 2103 atoms. 4454 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1978 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.1792 (Rfree = 0.000) for 2097 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1882 (Rfree = 0.000) for 2087 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.1764 (Rfree = 0.000) for 2085 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1678 (Rfree = 0.000) for 2087 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 2135 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 2146 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 8 peptides. Score 0.242 Round 2: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.399 Round 3: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.402 Round 4: 126 peptides, 21 chains. Longest chain 14 peptides. Score 0.448 Round 5: 122 peptides, 22 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 4 Chains 21, Residues 105, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4758 restraints for refining 2102 atoms. 4320 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1799 (Rfree = 0.000) for 2102 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 32: After refmac, R = 0.1671 (Rfree = 0.000) for 2091 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.1659 (Rfree = 0.000) for 2091 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1620 (Rfree = 0.000) for 2085 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 2083 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 2114 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2131 seeds are put forward Round 1: 104 peptides, 19 chains. Longest chain 14 peptides. Score 0.366 Round 2: 116 peptides, 19 chains. Longest chain 17 peptides. Score 0.440 Round 3: 121 peptides, 20 chains. Longest chain 15 peptides. Score 0.444 Round 4: 125 peptides, 19 chains. Longest chain 24 peptides. Score 0.492 Round 5: 131 peptides, 21 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 4 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4595 restraints for refining 2103 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1777 (Rfree = 0.000) for 2103 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.1527 (Rfree = 0.000) for 2097 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.1514 (Rfree = 0.000) for 2090 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1499 (Rfree = 0.000) for 2085 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1505 (Rfree = 0.000) for 2080 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 2095 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2117 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 12 peptides. Score 0.300 Round 2: 112 peptides, 20 chains. Longest chain 12 peptides. Score 0.389 Round 3: 109 peptides, 21 chains. Longest chain 10 peptides. Score 0.343 Round 4: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.357 Round 5: 101 peptides, 18 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 2 Chains 20, Residues 92, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3329 reflections ( 99.70 % complete ) and 4856 restraints for refining 2101 atoms. 4489 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1877 (Rfree = 0.000) for 2101 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.1843 (Rfree = 0.000) for 2101 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1760 (Rfree = 0.000) for 2104 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1692 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1831 (Rfree = 0.000) for 2107 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2159 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 12 peptides. Score 0.314 Round 2: 109 peptides, 20 chains. Longest chain 14 peptides. Score 0.370 Round 3: 114 peptides, 20 chains. Longest chain 14 peptides. Score 0.402 Round 4: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.414 Round 5: 116 peptides, 19 chains. Longest chain 18 peptides. Score 0.440 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 97, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3329 reflections ( 99.70 % complete ) and 4795 restraints for refining 2103 atoms. 4388 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2297 (Rfree = 0.000) for 2103 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2256 (Rfree = 0.000) for 2081 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2098 (Rfree = 0.000) for 2066 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1709 (Rfree = 0.000) for 2056 atoms. TimeTaking 27.23