Mon 7 Jan 11:15:01 GMT 2019 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p4o-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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/2p4o-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 ============================================================ Mon 7 Jan 11:16:04 GMT 2019 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/2p4o-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 192 and 0 Target number of residues in the AU: 192 Target solvent content: 0.6689 Checking the provided sequence file Detected sequence length: 306 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 306 Adjusted target solvent content: 0.47 Input MTZ file: 2p4o-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: 94 Cell parameters: 91.400 91.400 75.131 90.000 90.000 90.000 Input sequence file: 2p4o-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.686 3.800 Wilson plot Bfac: 90.42 3406 reflections ( 99.68 % complete ) and 0 restraints for refining 2720 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3535 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3522 (Rfree = 0.000) for 2720 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.92 Search for helices and strands: 0 residues in 0 chains, 2734 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.238 Round 2: 100 peptides, 20 chains. Longest chain 11 peptides. Score 0.291 Round 3: 137 peptides, 24 chains. Longest chain 15 peptides. Score 0.399 Round 4: 157 peptides, 27 chains. Longest chain 12 peptides. Score 0.434 Round 5: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.499 Taking the results from Round 5 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 5221 restraints for refining 2213 atoms. 4672 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3248 (Rfree = 0.000) for 2213 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 2: After refmac, R = 0.2912 (Rfree = 0.000) for 2155 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 3: After refmac, R = 0.2827 (Rfree = 0.000) for 2109 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 4: After refmac, R = 0.2682 (Rfree = 0.000) for 2084 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2720 (Rfree = 0.000) for 2065 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.90 Search for helices and strands: 0 residues in 0 chains, 2148 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 10 peptides. Score 0.297 Round 2: 136 peptides, 23 chains. Longest chain 10 peptides. Score 0.416 Round 3: 139 peptides, 25 chains. Longest chain 10 peptides. Score 0.387 Round 4: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.450 Round 5: 136 peptides, 21 chains. Longest chain 15 peptides. Score 0.458 Taking the results from Round 5 Chains 21, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 5004 restraints for refining 2093 atoms. 4565 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2709 (Rfree = 0.000) for 2093 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2535 (Rfree = 0.000) for 2066 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 8: After refmac, R = 0.2087 (Rfree = 0.000) for 2054 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2602 (Rfree = 0.000) for 2048 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 10: After refmac, R = 0.2506 (Rfree = 0.000) for 2034 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.85 Search for helices and strands: 0 residues in 0 chains, 2106 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 7 peptides. Score 0.283 Round 2: 135 peptides, 26 chains. Longest chain 11 peptides. Score 0.344 Round 3: 146 peptides, 25 chains. Longest chain 13 peptides. Score 0.423 Round 4: 145 peptides, 24 chains. Longest chain 17 peptides. Score 0.439 Round 5: 148 peptides, 25 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Chains 24, Residues 121, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4721 restraints for refining 2093 atoms. 4195 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2705 (Rfree = 0.000) for 2093 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.2716 (Rfree = 0.000) for 2057 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 13: After refmac, R = 0.2714 (Rfree = 0.000) for 2026 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 14: After refmac, R = 0.2660 (Rfree = 0.000) for 2009 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.2693 (Rfree = 0.000) for 1992 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.78 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 9 peptides. Score 0.269 Round 2: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.390 Round 3: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.387 Round 4: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.356 Round 5: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.418 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4847 restraints for refining 2073 atoms. 4466 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2610 (Rfree = 0.000) for 2073 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 17: After refmac, R = 0.2585 (Rfree = 0.000) for 2046 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 18: After refmac, R = 0.2605 (Rfree = 0.000) for 2029 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 19: After refmac, R = 0.2527 (Rfree = 0.000) for 2017 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2539 (Rfree = 0.000) for 2006 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.85 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 10 peptides. Score 0.268 Round 2: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.356 Round 3: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.381 Round 4: 120 peptides, 18 chains. Longest chain 15 peptides. Score 0.445 Round 5: 125 peptides, 21 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 4 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4348 restraints for refining 1985 atoms. 3906 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2628 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 22: After refmac, R = 0.2577 (Rfree = 0.000) for 1962 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 1949 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1839 (Rfree = 0.000) for 1951 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2328 (Rfree = 0.000) for 1949 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.88 Search for helices and strands: 0 residues in 0 chains, 1981 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.318 Round 2: 116 peptides, 20 chains. Longest chain 14 peptides. Score 0.380 Round 3: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.424 Round 4: 129 peptides, 19 chains. Longest chain 16 peptides. Score 0.467 Round 5: 128 peptides, 21 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 4 Chains 19, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4522 restraints for refining 2013 atoms. 4101 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2195 (Rfree = 0.000) for 2013 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2310 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2166 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2187 (Rfree = 0.000) for 1993 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.2204 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.80 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.274 Round 2: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.349 Round 3: 116 peptides, 21 chains. Longest chain 14 peptides. Score 0.356 Round 4: 125 peptides, 20 chains. Longest chain 16 peptides. Score 0.426 Round 5: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4489 restraints for refining 2032 atoms. 4074 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2721 (Rfree = 0.000) for 2032 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 32: After refmac, R = 0.2507 (Rfree = 0.000) for 2021 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.2343 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.2374 (Rfree = 0.000) for 1988 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2079 (Rfree = 0.000) for 1985 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.89 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 15 peptides. Score 0.291 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.293 Round 3: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.315 Round 4: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Round 5: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.329 Taking the results from Round 4 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 4300 restraints for refining 1900 atoms. 3996 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2514 (Rfree = 0.000) for 1900 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2279 (Rfree = 0.000) for 1891 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2370 (Rfree = 0.000) for 1884 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2403 (Rfree = 0.000) for 1879 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2473 (Rfree = 0.000) for 1872 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.81 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.214 Round 2: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.259 Round 3: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.277 Round 4: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.328 Round 5: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3406 reflections ( 99.68 % complete ) and 3863 restraints for refining 1768 atoms. 3624 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2291 (Rfree = 0.000) for 1768 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 42: After refmac, R = 0.2061 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2006 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.2640 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 45: After refmac, R = 0.2063 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.86 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.208 Round 2: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.262 Round 3: 84 peptides, 16 chains. Longest chain 10 peptides. Score 0.297 Round 4: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.279 Round 5: 82 peptides, 16 chains. Longest chain 10 peptides. Score 0.285 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 68, 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 2p4o-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3406 reflections ( 99.68 % complete ) and 3765 restraints for refining 1736 atoms. 3509 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2077 (Rfree = 0.000) for 1736 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1918 (Rfree = 0.000) for 1728 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2052 (Rfree = 0.000) for 1719 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1947 (Rfree = 0.000) for 1711 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 34.7