Sun 23 Dec 23:44:16 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 2ouw-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-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/2ouw-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-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 ============================================================ Sun 23 Dec 23:44:21 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/2ouw-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.4-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 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.6455 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.4-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2208 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: 108.355 3.400 Wilson plot Bfac: 74.07 3938 reflections ( 99.82 % complete ) and 0 restraints for refining 2460 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3487 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3204 (Rfree = 0.000) for 2460 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 2517 seeds are put forward NCS extension: 0 residues added, 2517 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.257 Round 2: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.441 Round 3: 133 peptides, 20 chains. Longest chain 14 peptides. Score 0.521 Round 4: 141 peptides, 20 chains. Longest chain 14 peptides. Score 0.564 Round 5: 142 peptides, 18 chains. Longest chain 15 peptides. Score 0.612 Taking the results from Round 5 Chains 18, Residues 124, Estimated correctness of the model 32.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4412 restraints for refining 2003 atoms. 3882 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2942 (Rfree = 0.000) for 2003 atoms. Found 11 (15 requested) and removed 45 (7 requested) atoms. Cycle 2: After refmac, R = 0.2963 (Rfree = 0.000) for 1928 atoms. Found 13 (14 requested) and removed 35 (7 requested) atoms. Cycle 3: After refmac, R = 0.2526 (Rfree = 0.000) for 1879 atoms. Found 11 (14 requested) and removed 28 (7 requested) atoms. Cycle 4: After refmac, R = 0.2701 (Rfree = 0.000) for 1856 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 5: After refmac, R = 0.2747 (Rfree = 0.000) for 1847 atoms. Found 12 (13 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 1901 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 1910 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.288 Round 2: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.393 Round 3: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.454 Round 4: 120 peptides, 18 chains. Longest chain 15 peptides. Score 0.498 Round 5: 113 peptides, 18 chains. Longest chain 10 peptides. Score 0.456 Taking the results from Round 4 Chains 18, Residues 102, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4236 restraints for refining 1879 atoms. 3832 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2724 (Rfree = 0.000) for 1879 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. Cycle 7: After refmac, R = 0.2623 (Rfree = 0.000) for 1836 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.2522 (Rfree = 0.000) for 1819 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.2408 (Rfree = 0.000) for 1812 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2497 (Rfree = 0.000) for 1807 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1918 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 8 peptides. Score 0.230 Round 2: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.393 Round 3: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.372 Round 4: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.468 Round 5: 118 peptides, 19 chains. Longest chain 14 peptides. Score 0.460 Taking the results from Round 4 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4531 restraints for refining 1948 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2656 (Rfree = 0.000) for 1948 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 12: After refmac, R = 0.2955 (Rfree = 0.000) for 1936 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.2774 (Rfree = 0.000) for 1927 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 14: After refmac, R = 0.2795 (Rfree = 0.000) for 1916 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.2833 (Rfree = 0.000) for 1910 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward NCS extension: 0 residues added, 2016 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.247 Round 2: 120 peptides, 20 chains. Longest chain 15 peptides. Score 0.446 Round 3: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.446 Round 4: 112 peptides, 18 chains. Longest chain 9 peptides. Score 0.450 Round 5: 115 peptides, 19 chains. Longest chain 9 peptides. Score 0.442 Taking the results from Round 4 Chains 18, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4467 restraints for refining 1938 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2907 (Rfree = 0.000) for 1938 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 17: After refmac, R = 0.2854 (Rfree = 0.000) for 1925 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.2928 (Rfree = 0.000) for 1916 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.2872 (Rfree = 0.000) for 1914 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 20: After refmac, R = 0.2930 (Rfree = 0.000) for 1914 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 2004 seeds are put forward NCS extension: 0 residues added, 2004 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.298 Round 2: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.398 Round 3: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.389 Round 4: 112 peptides, 18 chains. Longest chain 14 peptides. Score 0.450 Round 5: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.378 Taking the results from Round 4 Chains 18, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3938 reflections ( 99.82 % complete ) and 4444 restraints for refining 1941 atoms. 4086 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2932 (Rfree = 0.000) for 1941 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 22: After refmac, R = 0.2965 (Rfree = 0.000) for 1937 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 23: After refmac, R = 0.2607 (Rfree = 0.000) for 1929 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2547 (Rfree = 0.000) for 1927 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2547 (Rfree = 0.000) for 1919 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 1953 seeds are put forward NCS extension: 0 residues added, 1953 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 8 peptides. Score 0.258 Round 2: 98 peptides, 18 chains. Longest chain 8 peptides. Score 0.360 Round 3: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.297 Round 4: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.357 Round 5: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 2 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4575 restraints for refining 1980 atoms. 4273 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2864 (Rfree = 0.000) for 1980 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 27: After refmac, R = 0.2905 (Rfree = 0.000) for 1973 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2911 (Rfree = 0.000) for 1976 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.2843 (Rfree = 0.000) for 1976 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.2487 (Rfree = 0.000) for 1970 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 0 residues added, 2005 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.230 Round 2: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.332 Round 3: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.344 Round 4: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.362 Round 5: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4650 restraints for refining 2007 atoms. 4359 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2976 (Rfree = 0.000) for 2007 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.2835 (Rfree = 0.000) for 1998 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.2804 (Rfree = 0.000) for 1992 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 34: After refmac, R = 0.3146 (Rfree = 0.000) for 1988 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 35: After refmac, R = 0.2685 (Rfree = 0.000) for 1980 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 0 residues added, 2054 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 7 peptides. Score 0.209 Round 2: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.250 Round 3: 101 peptides, 23 chains. Longest chain 7 peptides. Score 0.234 Round 4: 114 peptides, 24 chains. Longest chain 7 peptides. Score 0.297 Round 5: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 5 Chains 21, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4540 restraints for refining 2005 atoms. 4213 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2597 (Rfree = 0.000) for 2005 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2492 (Rfree = 0.000) for 1994 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2490 (Rfree = 0.000) for 1999 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2523 (Rfree = 0.000) for 2000 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.2208 (Rfree = 0.000) for 2001 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.77 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 0 residues added, 2044 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 5 peptides. Score 0.220 Round 2: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.317 Round 3: 88 peptides, 18 chains. Longest chain 7 peptides. Score 0.290 Round 4: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.322 Round 5: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.314 Taking the results from Round 4 Chains 16, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3938 reflections ( 99.82 % complete ) and 4633 restraints for refining 2007 atoms. 4377 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2705 (Rfree = 0.000) for 2007 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.2591 (Rfree = 0.000) for 2008 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.2543 (Rfree = 0.000) for 2010 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2569 (Rfree = 0.000) for 2018 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2536 (Rfree = 0.000) for 2024 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.77 Search for helices and strands: 0 residues in 0 chains, 2095 seeds are put forward NCS extension: 0 residues added, 2095 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.230 Round 2: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.263 Round 3: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.324 Round 4: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.316 Round 5: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 65, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3938 reflections ( 99.82 % complete ) and 4618 restraints for refining 2007 atoms. 4373 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2691 (Rfree = 0.000) for 2007 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2674 (Rfree = 0.000) for 1993 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2485 (Rfree = 0.000) for 1983 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2520 (Rfree = 0.000) for 1972 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 31.38