Sun 23 Dec 22:22:50 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 2ghs-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-4.0-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/2ghs-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-4.0-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 22:22:59 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/2ghs-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-4.0-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 189 and 0 Target number of residues in the AU: 189 Target solvent content: 0.6418 Checking the provided sequence file Detected sequence length: 326 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 326 Adjusted target solvent content: 0.38 Input MTZ file: 2ghs-4.0-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: 19 Cell parameters: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 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: 55.478 4.000 Wilson plot Bfac: 72.11 2632 reflections ( 99.02 % complete ) and 0 restraints for refining 2888 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3449 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 2888 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2902 seeds are put forward Round 1: 82 peptides, 20 chains. Longest chain 5 peptides. Score 0.181 Round 2: 119 peptides, 23 chains. Longest chain 10 peptides. Score 0.338 Round 3: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.358 Round 4: 131 peptides, 24 chains. Longest chain 12 peptides. Score 0.383 Round 5: 132 peptides, 22 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 5 Chains 22, Residues 110, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 5738 restraints for refining 2353 atoms. 5297 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2699 (Rfree = 0.000) for 2353 atoms. Found 11 (11 requested) and removed 42 (5 requested) atoms. Cycle 2: After refmac, R = 0.2560 (Rfree = 0.000) for 2279 atoms. Found 7 (11 requested) and removed 23 (5 requested) atoms. Cycle 3: After refmac, R = 0.2466 (Rfree = 0.000) for 2238 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 4: After refmac, R = 0.2343 (Rfree = 0.000) for 2202 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2378 (Rfree = 0.000) for 2182 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 4.28 Search for helices and strands: 0 residues in 0 chains, 2237 seeds are put forward Round 1: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.295 Round 2: 128 peptides, 23 chains. Longest chain 10 peptides. Score 0.390 Round 3: 133 peptides, 24 chains. Longest chain 10 peptides. Score 0.394 Round 4: 125 peptides, 19 chains. Longest chain 14 peptides. Score 0.467 Round 5: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.470 Taking the results from Round 5 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4971 restraints for refining 2094 atoms. 4536 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2655 (Rfree = 0.000) for 2094 atoms. Found 9 (9 requested) and removed 34 (4 requested) atoms. Cycle 7: After refmac, R = 0.2163 (Rfree = 0.000) for 2043 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.2144 (Rfree = 0.000) for 2025 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.1933 (Rfree = 0.000) for 2008 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2172 (Rfree = 0.000) for 2003 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 13 peptides. Score 0.309 Round 2: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.370 Round 3: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.415 Round 4: 114 peptides, 15 chains. Longest chain 21 peptides. Score 0.502 Round 5: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.437 Taking the results from Round 4 Chains 16, Residues 99, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4712 restraints for refining 2052 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2461 (Rfree = 0.000) for 2052 atoms. Found 9 (9 requested) and removed 44 (4 requested) atoms. Cycle 12: After refmac, R = 0.2249 (Rfree = 0.000) for 1995 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2011 (Rfree = 0.000) for 1975 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.1836 (Rfree = 0.000) for 1965 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1985 (Rfree = 0.000) for 1957 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 10 peptides. Score 0.313 Round 2: 119 peptides, 22 chains. Longest chain 11 peptides. Score 0.363 Round 3: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.439 Round 4: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.381 Round 5: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 3 Chains 20, Residues 104, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4519 restraints for refining 1991 atoms. 4094 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2163 (Rfree = 0.000) for 1991 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 17: After refmac, R = 0.2084 (Rfree = 0.000) for 1969 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 18: After refmac, R = 0.1912 (Rfree = 0.000) for 1955 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.1443 (Rfree = 0.000) for 1948 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.1636 (Rfree = 0.000) for 1937 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 1977 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.284 Round 2: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.395 Round 3: 136 peptides, 24 chains. Longest chain 10 peptides. Score 0.410 Round 4: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.406 Round 5: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.413 Taking the results from Round 5 Chains 22, Residues 106, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4584 restraints for refining 2036 atoms. 4169 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2373 (Rfree = 0.000) for 2036 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 22: After refmac, R = 0.1953 (Rfree = 0.000) for 2010 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.1634 (Rfree = 0.000) for 2004 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.1400 (Rfree = 0.000) for 1994 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1261 (Rfree = 0.000) for 1987 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 4.24 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 7 peptides. Score 0.214 Round 2: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.360 Round 3: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.346 Round 4: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.389 Round 5: 105 peptides, 17 chains. Longest chain 10 peptides. Score 0.406 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4789 restraints for refining 2030 atoms. 4454 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1980 (Rfree = 0.000) for 2030 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2361 (Rfree = 0.000) for 2012 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.1977 (Rfree = 0.000) for 1997 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2102 (Rfree = 0.000) for 1993 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 30: After refmac, R = 0.1950 (Rfree = 0.000) for 1979 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.228 Round 2: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.344 Round 3: 126 peptides, 23 chains. Longest chain 12 peptides. Score 0.378 Round 4: 131 peptides, 25 chains. Longest chain 9 peptides. Score 0.359 Round 5: 131 peptides, 24 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 24, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4616 restraints for refining 2016 atoms. 4212 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2035 (Rfree = 0.000) for 2016 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 32: After refmac, R = 0.2028 (Rfree = 0.000) for 1994 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 33: After refmac, R = 0.1890 (Rfree = 0.000) for 1974 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 1962 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.1869 (Rfree = 0.000) for 1957 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 4.20 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.250 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.313 Round 3: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.352 Round 4: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.333 Round 5: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 5 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4694 restraints for refining 2041 atoms. 4395 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2096 (Rfree = 0.000) for 2041 atoms. Found 9 (9 requested) and removed 49 (4 requested) atoms. Cycle 37: After refmac, R = 0.2072 (Rfree = 0.000) for 1997 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2076 (Rfree = 0.000) for 1991 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 39: After refmac, R = 0.2007 (Rfree = 0.000) for 1975 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 40: After refmac, R = 0.2235 (Rfree = 0.000) for 1961 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2007 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.247 Round 2: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.318 Round 3: 108 peptides, 19 chains. Longest chain 9 peptides. Score 0.373 Round 4: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.312 Round 5: 93 peptides, 17 chains. Longest chain 8 peptides. Score 0.335 Taking the results from Round 3 Chains 19, Residues 89, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2632 reflections ( 99.02 % complete ) and 4325 restraints for refining 1998 atoms. 3950 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 1998 atoms. Found 9 (9 requested) and removed 34 (4 requested) atoms. Cycle 42: After refmac, R = 0.1924 (Rfree = 0.000) for 1959 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.1979 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 31 (4 requested) atoms. Cycle 44: After refmac, R = 0.1399 (Rfree = 0.000) for 1919 atoms. Found 3 (9 requested) and removed 16 (4 requested) atoms. Cycle 45: After refmac, R = 0.1285 (Rfree = 0.000) for 1902 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 4.07 Search for helices and strands: 0 residues in 0 chains, 1940 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.205 Round 2: 70 peptides, 15 chains. Longest chain 6 peptides. Score 0.240 Round 3: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.323 Round 4: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.346 Round 5: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 71, 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 2ghs-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2632 reflections ( 99.02 % complete ) and 4325 restraints for refining 1908 atoms. 4056 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1862 (Rfree = 0.000) for 1908 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2098 (Rfree = 0.000) for 1902 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1494 (Rfree = 0.000) for 1894 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2389 (Rfree = 0.000) for 1886 atoms. TimeTaking 34.07