null Sun 23 Dec 22:22:56 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 2hq7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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/2hq7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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 22:23:06 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/2hq7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.6-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6408 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.6-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2336 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: 89.671 3.600 Wilson plot Bfac: 72.21 3381 reflections ( 99.30 % complete ) and 0 restraints for refining 2582 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2888 (Rfree = 0.000) for 2582 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward NCS extension: 0 residues added, 2626 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.330 Round 2: 154 peptides, 22 chains. Longest chain 17 peptides. Score 0.547 Round 3: 167 peptides, 23 chains. Longest chain 15 peptides. Score 0.585 Round 4: 175 peptides, 22 chains. Longest chain 16 peptides. Score 0.636 Round 5: 192 peptides, 22 chains. Longest chain 17 peptides. Score 0.696 Taking the results from Round 5 Chains 22, Residues 170, Estimated correctness of the model 48.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4716 restraints for refining 2114 atoms. 4058 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2184 (Rfree = 0.000) for 2114 atoms. Found 11 (13 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.1998 (Rfree = 0.000) for 2080 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.1940 (Rfree = 0.000) for 2059 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.1904 (Rfree = 0.000) for 2042 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2014 (Rfree = 0.000) for 2033 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 2086 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2108 seeds are put forward Round 1: 143 peptides, 21 chains. Longest chain 14 peptides. Score 0.516 Round 2: 169 peptides, 21 chains. Longest chain 20 peptides. Score 0.630 Round 3: 166 peptides, 24 chains. Longest chain 17 peptides. Score 0.562 Round 4: 174 peptides, 21 chains. Longest chain 17 peptides. Score 0.649 Round 5: 178 peptides, 21 chains. Longest chain 24 peptides. Score 0.664 Taking the results from Round 5 Chains 21, Residues 157, Estimated correctness of the model 38.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4828 restraints for refining 2116 atoms. 4221 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2159 (Rfree = 0.000) for 2116 atoms. Found 10 (13 requested) and removed 14 (6 requested) atoms. Cycle 7: After refmac, R = 0.2050 (Rfree = 0.000) for 2091 atoms. Found 6 (13 requested) and removed 19 (6 requested) atoms. Cycle 8: After refmac, R = 0.2025 (Rfree = 0.000) for 2068 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1949 (Rfree = 0.000) for 2062 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1889 (Rfree = 0.000) for 2053 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 2137 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 2173 seeds are put forward Round 1: 130 peptides, 23 chains. Longest chain 12 peptides. Score 0.403 Round 2: 146 peptides, 20 chains. Longest chain 17 peptides. Score 0.551 Round 3: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.527 Round 4: 152 peptides, 21 chains. Longest chain 17 peptides. Score 0.558 Round 5: 155 peptides, 24 chains. Longest chain 14 peptides. Score 0.511 Taking the results from Round 4 Chains 21, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4944 restraints for refining 2113 atoms. 4441 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2053 (Rfree = 0.000) for 2113 atoms. Found 10 (13 requested) and removed 30 (6 requested) atoms. Cycle 12: After refmac, R = 0.2000 (Rfree = 0.000) for 2085 atoms. Found 8 (13 requested) and removed 18 (6 requested) atoms. Cycle 13: After refmac, R = 0.1928 (Rfree = 0.000) for 2067 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.1832 (Rfree = 0.000) for 2061 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1837 (Rfree = 0.000) for 2054 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2141 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 14 peptides. Score 0.367 Round 2: 147 peptides, 20 chains. Longest chain 15 peptides. Score 0.556 Round 3: 142 peptides, 18 chains. Longest chain 14 peptides. Score 0.574 Round 4: 146 peptides, 21 chains. Longest chain 14 peptides. Score 0.530 Round 5: 147 peptides, 19 chains. Longest chain 14 peptides. Score 0.576 Taking the results from Round 5 Chains 19, Residues 128, Estimated correctness of the model 5.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4877 restraints for refining 2117 atoms. 4384 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1834 (Rfree = 0.000) for 2117 atoms. Found 9 (13 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.1722 (Rfree = 0.000) for 2103 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1789 (Rfree = 0.000) for 2094 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1766 (Rfree = 0.000) for 2090 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1710 (Rfree = 0.000) for 2094 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 2158 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2172 seeds are put forward Round 1: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.360 Round 2: 128 peptides, 20 chains. Longest chain 13 peptides. Score 0.462 Round 3: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.434 Round 4: 137 peptides, 21 chains. Longest chain 12 peptides. Score 0.486 Round 5: 139 peptides, 21 chains. Longest chain 13 peptides. Score 0.496 Taking the results from Round 5 Chains 21, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4891 restraints for refining 2117 atoms. 4440 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1733 (Rfree = 0.000) for 2117 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.1550 (Rfree = 0.000) for 2107 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.1434 (Rfree = 0.000) for 2096 atoms. Found 1 (13 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.1507 (Rfree = 0.000) for 2086 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1393 (Rfree = 0.000) for 2078 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2154 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.332 Round 2: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.462 Round 3: 131 peptides, 17 chains. Longest chain 22 peptides. Score 0.544 Round 4: 133 peptides, 19 chains. Longest chain 22 peptides. Score 0.510 Round 5: 135 peptides, 22 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 3 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4896 restraints for refining 2117 atoms. 4426 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1898 (Rfree = 0.000) for 2117 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.1794 (Rfree = 0.000) for 2107 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.1806 (Rfree = 0.000) for 2104 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.1739 (Rfree = 0.000) for 2098 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.1707 (Rfree = 0.000) for 2092 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.67 Search for helices and strands: 0 residues in 0 chains, 2140 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2143 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 11 peptides. Score 0.309 Round 2: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.396 Round 3: 140 peptides, 21 chains. Longest chain 15 peptides. Score 0.501 Round 4: 141 peptides, 22 chains. Longest chain 21 peptides. Score 0.484 Round 5: 147 peptides, 22 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 5 Chains 22, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4903 restraints for refining 2117 atoms. 4425 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 2117 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.1852 (Rfree = 0.000) for 2107 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1815 (Rfree = 0.000) for 2106 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.1836 (Rfree = 0.000) for 2101 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1727 (Rfree = 0.000) for 2105 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.76 Search for helices and strands: 0 residues in 0 chains, 2157 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2179 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 10 peptides. Score 0.255 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.306 Round 3: 116 peptides, 17 chains. Longest chain 17 peptides. Score 0.469 Round 4: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.408 Round 5: 112 peptides, 18 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 3 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 5090 restraints for refining 2117 atoms. 4711 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1827 (Rfree = 0.000) for 2117 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.1744 (Rfree = 0.000) for 2116 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.1779 (Rfree = 0.000) for 2114 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1702 (Rfree = 0.000) for 2113 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1752 (Rfree = 0.000) for 2109 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 2155 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 2184 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.313 Round 2: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.385 Round 3: 120 peptides, 20 chains. Longest chain 10 peptides. Score 0.419 Round 4: 120 peptides, 19 chains. Longest chain 17 peptides. Score 0.443 Round 5: 127 peptides, 17 chains. Longest chain 20 peptides. Score 0.525 Taking the results from Round 5 Chains 17, Residues 110, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3381 reflections ( 99.30 % complete ) and 4729 restraints for refining 2116 atoms. 4237 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1893 (Rfree = 0.000) for 2116 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. Cycle 42: After refmac, R = 0.1835 (Rfree = 0.000) for 2102 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1768 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1682 (Rfree = 0.000) for 2095 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.1652 (Rfree = 0.000) for 2088 atoms. Found 12 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 2175 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2205 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.282 Round 2: 97 peptides, 17 chains. Longest chain 8 peptides. Score 0.361 Round 3: 102 peptides, 18 chains. Longest chain 8 peptides. Score 0.365 Round 4: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.365 Round 5: 106 peptides, 18 chains. Longest chain 7 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 88, 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 2hq7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3381 reflections ( 99.30 % complete ) and 5010 restraints for refining 2117 atoms. 4676 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1720 (Rfree = 0.000) for 2117 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1670 (Rfree = 0.000) for 2107 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1576 (Rfree = 0.000) for 2097 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1286 (Rfree = 0.000) for 2083 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:56 GMT 2018 Job finished. TimeTaking 43.01 Used memory is bytes: 13649112