null Sun 23 Dec 22:22:55 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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/2ghs-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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 ============================================================ Sun 23 Dec 22:23:04 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-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: 0.6361 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-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: 19 Cell parameters: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.60 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 3.801 Wilson plot Bfac: 69.51 3056 reflections ( 99.16 % complete ) and 0 restraints for refining 2895 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3405 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3168 (Rfree = 0.000) for 2895 atoms. Found 13 (15 requested) and removed 41 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 4.07 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.285 Round 2: 122 peptides, 25 chains. Longest chain 9 peptides. Score 0.306 Round 3: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.332 Round 4: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.401 Round 5: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 4 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 5757 restraints for refining 2358 atoms. 5327 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2812 (Rfree = 0.000) for 2358 atoms. Found 5 (12 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.2576 (Rfree = 0.000) for 2296 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2619 (Rfree = 0.000) for 2274 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 4: After refmac, R = 0.2507 (Rfree = 0.000) for 2260 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2488 (Rfree = 0.000) for 2250 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 2307 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.245 Round 2: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.358 Round 3: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.358 Round 4: 117 peptides, 18 chains. Longest chain 14 peptides. Score 0.448 Round 5: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 4 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4900 restraints for refining 2145 atoms. 4487 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 2145 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 7: After refmac, R = 0.2202 (Rfree = 0.000) for 2119 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2324 (Rfree = 0.000) for 2110 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2106 (Rfree = 0.000) for 2096 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 10: After refmac, R = 0.2090 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 4.06 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.298 Round 2: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.389 Round 3: 111 peptides, 16 chains. Longest chain 14 peptides. Score 0.463 Round 4: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.381 Round 5: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.426 Taking the results from Round 3 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4624 restraints for refining 2071 atoms. 4197 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2190 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2126 (Rfree = 0.000) for 2045 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 13: After refmac, R = 0.1966 (Rfree = 0.000) for 2031 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1884 (Rfree = 0.000) for 2023 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.1848 (Rfree = 0.000) for 2017 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 11 peptides. Score 0.287 Round 2: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.408 Round 3: 123 peptides, 22 chains. Longest chain 12 peptides. Score 0.386 Round 4: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.369 Round 5: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 2 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4471 restraints for refining 2048 atoms. 4069 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1947 (Rfree = 0.000) for 2048 atoms. Found 10 (11 requested) and removed 21 (5 requested) atoms. Cycle 17: After refmac, R = 0.1857 (Rfree = 0.000) for 2033 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.1894 (Rfree = 0.000) for 2027 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 19: After refmac, R = 0.1426 (Rfree = 0.000) for 2018 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1208 (Rfree = 0.000) for 2013 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2086 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 9 peptides. Score 0.288 Round 2: 114 peptides, 20 chains. Longest chain 13 peptides. Score 0.383 Round 3: 109 peptides, 19 chains. Longest chain 14 peptides. Score 0.379 Round 4: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.366 Round 5: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.353 Taking the results from Round 2 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4589 restraints for refining 2055 atoms. 4233 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1731 (Rfree = 0.000) for 2055 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 22: After refmac, R = 0.1519 (Rfree = 0.000) for 2038 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.1723 (Rfree = 0.000) for 2032 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 24: After refmac, R = 0.1574 (Rfree = 0.000) for 2026 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.1613 (Rfree = 0.000) for 2022 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.93 Search for helices and strands: 0 residues in 0 chains, 2098 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 10 peptides. Score 0.273 Round 2: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.326 Round 3: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.360 Round 4: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.375 Round 5: 102 peptides, 16 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 5 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4827 restraints for refining 2115 atoms. 4499 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1949 (Rfree = 0.000) for 2115 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.1848 (Rfree = 0.000) for 2103 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 28: After refmac, R = 0.1911 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.1266 (Rfree = 0.000) for 2087 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.1194 (Rfree = 0.000) for 2087 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 2161 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 9 peptides. Score 0.266 Round 2: 109 peptides, 19 chains. Longest chain 12 peptides. Score 0.379 Round 3: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.311 Round 4: 114 peptides, 19 chains. Longest chain 13 peptides. Score 0.408 Round 5: 120 peptides, 21 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 4 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4905 restraints for refining 2175 atoms. 4534 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1824 (Rfree = 0.000) for 2175 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.1860 (Rfree = 0.000) for 2158 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2034 (Rfree = 0.000) for 2146 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.1969 (Rfree = 0.000) for 2138 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.1929 (Rfree = 0.000) for 2137 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.188 Round 2: 98 peptides, 19 chains. Longest chain 10 peptides. Score 0.313 Round 3: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.313 Round 4: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.312 Round 5: 86 peptides, 18 chains. Longest chain 6 peptides. Score 0.264 Taking the results from Round 3 Chains 19, Residues 79, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4783 restraints for refining 2116 atoms. 4472 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2100 (Rfree = 0.000) for 2116 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 37: After refmac, R = 0.1788 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.1710 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1795 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 7 peptides. Score 0.244 Round 2: 100 peptides, 21 chains. Longest chain 7 peptides. Score 0.273 Round 3: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.362 Round 4: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.338 Round 5: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 5 Chains 19, Residues 87, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3056 reflections ( 99.16 % complete ) and 4924 restraints for refining 2147 atoms. 4566 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1857 (Rfree = 0.000) for 2147 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.2005 (Rfree = 0.000) for 2135 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.1662 (Rfree = 0.000) for 2123 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1832 (Rfree = 0.000) for 2120 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.1178 (Rfree = 0.000) for 2114 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.233 Round 2: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.340 Round 3: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.367 Round 4: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.382 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 70, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3056 reflections ( 99.16 % complete ) and 4920 restraints for refining 2089 atoms. 4653 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1998 (Rfree = 0.000) for 2089 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2058 (Rfree = 0.000) for 2081 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2319 (Rfree = 0.000) for 2070 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2058 (Rfree = 0.000) for 2057 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:27 GMT 2018 Job finished. TimeTaking 42.62 Used memory is bytes: 20413760