Tue 25 Dec 19:27:57 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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 ============================================================ Tue 25 Dec 19:28:07 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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 169 and 0 Target number of residues in the AU: 169 Target solvent content: 0.6421 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-3.8-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-3.8-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 3.801 Wilson plot Bfac: 72.44 2845 reflections ( 99.65 % complete ) and 0 restraints for refining 2584 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3449 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3157 (Rfree = 0.000) for 2584 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 2579 seeds are put forward NCS extension: 0 residues added, 2579 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.269 Round 2: 122 peptides, 22 chains. Longest chain 14 peptides. Score 0.399 Round 3: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.391 Round 4: 141 peptides, 23 chains. Longest chain 14 peptides. Score 0.485 Round 5: 146 peptides, 22 chains. Longest chain 12 peptides. Score 0.534 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4662 restraints for refining 2097 atoms. 4156 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2330 (Rfree = 0.000) for 2097 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2336 (Rfree = 0.000) for 2076 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2338 (Rfree = 0.000) for 2061 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 2043 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2433 (Rfree = 0.000) for 2035 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 2093 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2108 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 6 peptides. Score 0.265 Round 2: 117 peptides, 23 chains. Longest chain 7 peptides. Score 0.340 Round 3: 125 peptides, 24 chains. Longest chain 8 peptides. Score 0.365 Round 4: 126 peptides, 23 chains. Longest chain 9 peptides. Score 0.397 Round 5: 142 peptides, 23 chains. Longest chain 12 peptides. Score 0.490 Taking the results from Round 5 Chains 24, Residues 119, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4732 restraints for refining 2098 atoms. 4198 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2215 (Rfree = 0.000) for 2098 atoms. Found 5 (11 requested) and removed 19 (5 requested) atoms. Cycle 7: After refmac, R = 0.2157 (Rfree = 0.000) for 2064 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2096 (Rfree = 0.000) for 2050 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2403 (Rfree = 0.000) for 2038 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.1556 (Rfree = 0.000) for 2031 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2091 seeds are put forward NCS extension: 0 residues added, 2091 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 7 peptides. Score 0.305 Round 2: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.432 Round 3: 141 peptides, 26 chains. Longest chain 11 peptides. Score 0.411 Round 4: 152 peptides, 25 chains. Longest chain 12 peptides. Score 0.498 Round 5: 149 peptides, 25 chains. Longest chain 10 peptides. Score 0.481 Taking the results from Round 4 Chains 25, Residues 127, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4743 restraints for refining 2098 atoms. 4207 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2077 (Rfree = 0.000) for 2098 atoms. Found 5 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.1936 (Rfree = 0.000) for 2082 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1800 (Rfree = 0.000) for 2075 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1751 (Rfree = 0.000) for 2066 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.1770 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 2121 seeds are put forward NCS extension: 0 residues added, 2121 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.243 Round 2: 95 peptides, 19 chains. Longest chain 13 peptides. Score 0.306 Round 3: 106 peptides, 21 chains. Longest chain 7 peptides. Score 0.323 Round 4: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.414 Round 5: 103 peptides, 16 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 16, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 5096 restraints for refining 2098 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1814 (Rfree = 0.000) for 2098 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2256 (Rfree = 0.000) for 2080 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.1781 (Rfree = 0.000) for 2072 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1975 (Rfree = 0.000) for 2068 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1929 (Rfree = 0.000) for 2067 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2163 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.190 Round 2: 102 peptides, 21 chains. Longest chain 7 peptides. Score 0.296 Round 3: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.367 Round 4: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.353 Round 5: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 3 Chains 22, Residues 95, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4783 restraints for refining 2076 atoms. 4386 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1648 (Rfree = 0.000) for 2076 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1458 (Rfree = 0.000) for 2065 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.1540 (Rfree = 0.000) for 2062 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1733 (Rfree = 0.000) for 2064 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1880 (Rfree = 0.000) for 2060 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 2115 seeds are put forward NCS extension: 0 residues added, 2115 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.292 Round 2: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.391 Round 3: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.378 Round 4: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.374 Round 5: 97 peptides, 17 chains. Longest chain 9 peptides. Score 0.376 Taking the results from Round 2 Chains 19, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2845 reflections ( 99.65 % complete ) and 4664 restraints for refining 2040 atoms. 4327 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2022 (Rfree = 0.000) for 2040 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.1970 (Rfree = 0.000) for 2030 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.1900 (Rfree = 0.000) for 2024 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1865 (Rfree = 0.000) for 2019 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.1158 (Rfree = 0.000) for 2017 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward NCS extension: 0 residues added, 2063 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 5 peptides. Score 0.204 Round 2: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.260 Round 3: 104 peptides, 22 chains. Longest chain 7 peptides. Score 0.281 Round 4: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.369 Round 5: 126 peptides, 23 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 5 Chains 23, Residues 103, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4620 restraints for refining 2055 atoms. 4217 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1637 (Rfree = 0.000) for 2055 atoms. Found 5 (11 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.1515 (Rfree = 0.000) for 2040 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1196 (Rfree = 0.000) for 2034 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1116 (Rfree = 0.000) for 2029 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1167 (Rfree = 0.000) for 2022 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward NCS extension: 0 residues added, 2067 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 6 peptides. Score 0.255 Round 2: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.314 Round 3: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.324 Round 4: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.397 Round 5: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4790 restraints for refining 2098 atoms. 4420 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1973 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2093 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 2079 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2062 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 2069 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 2125 seeds are put forward NCS extension: 0 residues added, 2125 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.228 Round 2: 87 peptides, 18 chains. Longest chain 9 peptides. Score 0.279 Round 3: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.307 Round 4: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.363 Round 5: 103 peptides, 20 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 4 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4723 restraints for refining 2036 atoms. 4428 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1944 (Rfree = 0.000) for 2036 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2020 (Rfree = 0.000) for 2030 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2214 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1405 (Rfree = 0.000) for 2021 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1277 (Rfree = 0.000) for 2024 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 0 residues added, 2047 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.227 Round 2: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.263 Round 3: 68 peptides, 13 chains. Longest chain 8 peptides. Score 0.295 Round 4: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.291 Round 5: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.278 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 55, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 13 chains (55 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2845 reflections ( 99.65 % complete ) and 4306 restraints for refining 1916 atoms. 4062 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1822 (Rfree = 0.000) for 1916 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1448 (Rfree = 0.000) for 1908 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1280 (Rfree = 0.000) for 1899 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1327 (Rfree = 0.000) for 1891 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:10:52 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 42.93