Sun 23 Dec 22:22:53 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 2oc5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.6-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/2oc5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.6-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 22:23:03 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/2oc5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.6-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6415 Checking the provided sequence file Detected sequence length: 244 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 244 Adjusted target solvent content: 0.62 Input MTZ file: 2oc5-3.6-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: 96 Cell parameters: 77.390 77.390 116.960 90.000 90.000 90.000 Input sequence file: 2oc5-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1952 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.240 3.600 Wilson plot Bfac: 72.53 4438 reflections ( 99.15 % complete ) and 0 restraints for refining 2151 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3256 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3206 (Rfree = 0.000) for 2151 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 2.94 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.319 Round 2: 136 peptides, 18 chains. Longest chain 16 peptides. Score 0.494 Round 3: 138 peptides, 15 chains. Longest chain 25 peptides. Score 0.558 Round 4: 140 peptides, 17 chains. Longest chain 18 peptides. Score 0.529 Round 5: 133 peptides, 17 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 3 Chains 19, Residues 123, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3556 restraints for refining 1770 atoms. 2956 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2501 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 2: After refmac, R = 0.2403 (Rfree = 0.000) for 1723 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2331 (Rfree = 0.000) for 1711 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2286 (Rfree = 0.000) for 1699 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2224 (Rfree = 0.000) for 1692 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.92 Search for helices and strands: 0 residues in 0 chains, 1783 seeds are put forward Round 1: 133 peptides, 20 chains. Longest chain 14 peptides. Score 0.443 Round 2: 143 peptides, 19 chains. Longest chain 19 peptides. Score 0.504 Round 3: 141 peptides, 17 chains. Longest chain 23 peptides. Score 0.533 Round 4: 132 peptides, 18 chains. Longest chain 18 peptides. Score 0.477 Round 5: 138 peptides, 18 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 3 Chains 17, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3951 restraints for refining 1736 atoms. 3472 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2461 (Rfree = 0.000) for 1736 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.2324 (Rfree = 0.000) for 1720 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2303 (Rfree = 0.000) for 1713 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2192 (Rfree = 0.000) for 1707 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2269 (Rfree = 0.000) for 1700 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.91 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward Round 1: 143 peptides, 20 chains. Longest chain 17 peptides. Score 0.486 Round 2: 146 peptides, 20 chains. Longest chain 17 peptides. Score 0.498 Round 3: 148 peptides, 19 chains. Longest chain 20 peptides. Score 0.524 Round 4: 142 peptides, 16 chains. Longest chain 19 peptides. Score 0.555 Round 5: 147 peptides, 20 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 4 Chains 16, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3997 restraints for refining 1770 atoms. 3509 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2403 (Rfree = 0.000) for 1770 atoms. Found 7 (11 requested) and removed 16 (5 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 1744 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2152 (Rfree = 0.000) for 1737 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2094 (Rfree = 0.000) for 1734 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2077 (Rfree = 0.000) for 1727 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 10 peptides. Score 0.412 Round 2: 153 peptides, 20 chains. Longest chain 25 peptides. Score 0.526 Round 3: 158 peptides, 22 chains. Longest chain 13 peptides. Score 0.510 Round 4: 148 peptides, 17 chains. Longest chain 20 peptides. Score 0.560 Round 5: 143 peptides, 20 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 4 Chains 19, Residues 131, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3697 restraints for refining 1770 atoms. 3123 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2439 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2285 (Rfree = 0.000) for 1752 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2209 (Rfree = 0.000) for 1748 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2108 (Rfree = 0.000) for 1739 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2022 (Rfree = 0.000) for 1735 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 2.90 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward Round 1: 137 peptides, 22 chains. Longest chain 13 peptides. Score 0.421 Round 2: 152 peptides, 21 chains. Longest chain 14 peptides. Score 0.504 Round 3: 145 peptides, 15 chains. Longest chain 23 peptides. Score 0.584 Round 4: 143 peptides, 15 chains. Longest chain 24 peptides. Score 0.576 Round 5: 153 peptides, 15 chains. Longest chain 32 peptides. Score 0.612 Taking the results from Round 5 Chains 18, Residues 138, Estimated correctness of the model 19.3 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3538 restraints for refining 1770 atoms. 2900 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2551 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2362 (Rfree = 0.000) for 1758 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2287 (Rfree = 0.000) for 1755 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2181 (Rfree = 0.000) for 1752 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.2138 (Rfree = 0.000) for 1747 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.91 Search for helices and strands: 0 residues in 0 chains, 1847 seeds are put forward Round 1: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.409 Round 2: 131 peptides, 16 chains. Longest chain 15 peptides. Score 0.511 Round 3: 144 peptides, 15 chains. Longest chain 23 peptides. Score 0.580 Round 4: 141 peptides, 15 chains. Longest chain 23 peptides. Score 0.569 Round 5: 143 peptides, 16 chains. Longest chain 19 peptides. Score 0.559 Taking the results from Round 3 Chains 17, Residues 129, Estimated correctness of the model 6.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3520 restraints for refining 1770 atoms. 2911 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2916 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 1754 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2300 (Rfree = 0.000) for 1748 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2235 (Rfree = 0.000) for 1742 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.2199 (Rfree = 0.000) for 1739 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.87 Search for helices and strands: 0 residues in 0 chains, 1835 seeds are put forward Round 1: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.365 Round 2: 138 peptides, 18 chains. Longest chain 14 peptides. Score 0.502 Round 3: 137 peptides, 15 chains. Longest chain 23 peptides. Score 0.554 Round 4: 132 peptides, 16 chains. Longest chain 19 peptides. Score 0.516 Round 5: 135 peptides, 17 chains. Longest chain 20 peptides. Score 0.509 Taking the results from Round 3 Chains 17, Residues 122, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3903 restraints for refining 1770 atoms. 3397 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2401 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 32: After refmac, R = 0.2249 (Rfree = 0.000) for 1746 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2165 (Rfree = 0.000) for 1737 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2103 (Rfree = 0.000) for 1735 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2029 (Rfree = 0.000) for 1731 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 127 peptides, 22 chains. Longest chain 16 peptides. Score 0.374 Round 2: 144 peptides, 20 chains. Longest chain 16 peptides. Score 0.490 Round 3: 138 peptides, 22 chains. Longest chain 19 peptides. Score 0.425 Round 4: 138 peptides, 21 chains. Longest chain 16 peptides. Score 0.445 Round 5: 138 peptides, 20 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 2 Chains 20, Residues 124, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 3707 restraints for refining 1770 atoms. 3186 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2176 (Rfree = 0.000) for 1770 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2057 (Rfree = 0.000) for 1760 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 1755 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1991 (Rfree = 0.000) for 1751 atoms. Found 2 (11 requested) and removed 12 (5 requested) atoms. Cycle 40: After refmac, R = 0.1960 (Rfree = 0.000) for 1738 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 2.87 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.333 Round 2: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.389 Round 3: 119 peptides, 21 chains. Longest chain 12 peptides. Score 0.357 Round 4: 137 peptides, 21 chains. Longest chain 15 peptides. Score 0.441 Round 5: 136 peptides, 21 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 4 Chains 21, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4438 reflections ( 99.15 % complete ) and 4048 restraints for refining 1769 atoms. 3605 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2295 (Rfree = 0.000) for 1769 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.2250 (Rfree = 0.000) for 1765 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 43: After refmac, R = 0.2160 (Rfree = 0.000) for 1754 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2146 (Rfree = 0.000) for 1755 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.2150 (Rfree = 0.000) for 1753 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 2.89 Search for helices and strands: 0 residues in 0 chains, 1854 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.309 Round 2: 114 peptides, 18 chains. Longest chain 11 peptides. Score 0.396 Round 3: 118 peptides, 18 chains. Longest chain 11 peptides. Score 0.415 Round 4: 115 peptides, 15 chains. Longest chain 16 peptides. Score 0.463 Round 5: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 100, 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 2oc5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4438 reflections ( 99.15 % complete ) and 4078 restraints for refining 1770 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2459 (Rfree = 0.000) for 1770 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 1755 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2279 (Rfree = 0.000) for 1748 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 1741 atoms. TimeTaking 33.15