null Sun 23 Dec 22:23:02 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 2pw4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.2-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/2pw4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.2-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 22:23:11 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/2pw4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.2-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 147 and 0 Target number of residues in the AU: 147 Target solvent content: 0.6195 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 188 Adjusted target solvent content: 0.51 Input MTZ file: 2pw4-3.2-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: 5 Cell parameters: 77.750 59.670 57.820 90.000 128.790 90.000 Input sequence file: 2pw4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1504 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: 25.783 3.200 Wilson plot Bfac: 60.84 3403 reflections ( 97.79 % complete ) and 0 restraints for refining 1675 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3095 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2408 (Rfree = 0.000) for 1675 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 1728 seeds are put forward Round 1: 103 peptides, 19 chains. Longest chain 12 peptides. Score 0.391 Round 2: 121 peptides, 20 chains. Longest chain 18 peptides. Score 0.489 Round 3: 122 peptides, 18 chains. Longest chain 21 peptides. Score 0.551 Round 4: 127 peptides, 15 chains. Longest chain 31 peptides. Score 0.654 Round 5: 131 peptides, 15 chains. Longest chain 23 peptides. Score 0.673 Taking the results from Round 5 Chains 15, Residues 116, Estimated correctness of the model 59.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2915 restraints for refining 1373 atoms. 2466 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2362 (Rfree = 0.000) for 1373 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2224 (Rfree = 0.000) for 1364 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 3: After refmac, R = 0.2045 (Rfree = 0.000) for 1362 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.1975 (Rfree = 0.000) for 1357 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1967 (Rfree = 0.000) for 1352 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1405 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.466 Round 2: 122 peptides, 15 chains. Longest chain 17 peptides. Score 0.628 Round 3: 132 peptides, 13 chains. Longest chain 31 peptides. Score 0.719 Round 4: 119 peptides, 13 chains. Longest chain 22 peptides. Score 0.659 Round 5: 130 peptides, 17 chains. Longest chain 18 peptides. Score 0.622 Taking the results from Round 3 Chains 17, Residues 119, Estimated correctness of the model 69.1 % 4 chains (26 residues) have been docked in sequence Building loops using Loopy2018 17 chains (119 residues) following loop building 4 chains (26 residues) in sequence following loop building ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2690 restraints for refining 1373 atoms. 2145 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2396 (Rfree = 0.000) for 1373 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 1371 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 1367 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2107 (Rfree = 0.000) for 1364 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 1356 atoms. Found 3 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward Round 1: 111 peptides, 14 chains. Longest chain 14 peptides. Score 0.591 Round 2: 126 peptides, 14 chains. Longest chain 22 peptides. Score 0.671 Round 3: 123 peptides, 13 chains. Longest chain 32 peptides. Score 0.679 Round 4: 131 peptides, 15 chains. Longest chain 34 peptides. Score 0.673 Round 5: 129 peptides, 15 chains. Longest chain 22 peptides. Score 0.663 Taking the results from Round 3 Chains 15, Residues 110, Estimated correctness of the model 60.6 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2779 restraints for refining 1373 atoms. 2266 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2311 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2078 (Rfree = 0.000) for 1367 atoms. Found 11 (11 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2016 (Rfree = 0.000) for 1368 atoms. Found 5 (11 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1874 (Rfree = 0.000) for 1361 atoms. Found 5 (11 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.1871 (Rfree = 0.000) for 1352 atoms. Found 4 (11 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1394 seeds are put forward Round 1: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.482 Round 2: 119 peptides, 17 chains. Longest chain 14 peptides. Score 0.559 Round 3: 122 peptides, 15 chains. Longest chain 22 peptides. Score 0.628 Round 4: 122 peptides, 16 chains. Longest chain 22 peptides. Score 0.603 Round 5: 130 peptides, 14 chains. Longest chain 25 peptides. Score 0.690 Taking the results from Round 5 Chains 16, Residues 116, Estimated correctness of the model 63.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2755 restraints for refining 1373 atoms. 2229 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2367 (Rfree = 0.000) for 1373 atoms. Found 9 (11 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 1369 atoms. Found 5 (11 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.1955 (Rfree = 0.000) for 1363 atoms. Found 6 (11 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1827 (Rfree = 0.000) for 1362 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1800 (Rfree = 0.000) for 1357 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward Round 1: 111 peptides, 17 chains. Longest chain 14 peptides. Score 0.509 Round 2: 126 peptides, 19 chains. Longest chain 15 peptides. Score 0.549 Round 3: 122 peptides, 16 chains. Longest chain 18 peptides. Score 0.603 Round 4: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.563 Round 5: 125 peptides, 18 chains. Longest chain 17 peptides. Score 0.569 Taking the results from Round 3 Chains 16, Residues 106, Estimated correctness of the model 41.9 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2752 restraints for refining 1373 atoms. 2263 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2315 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 1368 atoms. Found 3 (11 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1953 (Rfree = 0.000) for 1363 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1904 (Rfree = 0.000) for 1357 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1876 (Rfree = 0.000) for 1353 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.378 Round 2: 95 peptides, 14 chains. Longest chain 16 peptides. Score 0.490 Round 3: 114 peptides, 17 chains. Longest chain 15 peptides. Score 0.528 Round 4: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.550 Round 5: 115 peptides, 15 chains. Longest chain 17 peptides. Score 0.588 Taking the results from Round 5 Chains 15, Residues 100, Estimated correctness of the model 37.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 3069 restraints for refining 1373 atoms. 2684 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2147 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.1993 (Rfree = 0.000) for 1373 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1944 (Rfree = 0.000) for 1369 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1902 (Rfree = 0.000) for 1365 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1871 (Rfree = 0.000) for 1360 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward Round 1: 88 peptides, 14 chains. Longest chain 15 peptides. Score 0.440 Round 2: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.480 Round 3: 97 peptides, 15 chains. Longest chain 11 peptides. Score 0.473 Round 4: 102 peptides, 14 chains. Longest chain 14 peptides. Score 0.536 Round 5: 99 peptides, 14 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 4 Chains 14, Residues 88, Estimated correctness of the model 22.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 3040 restraints for refining 1373 atoms. 2679 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2177 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 1378 atoms. Found 3 (11 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.1923 (Rfree = 0.000) for 1375 atoms. Found 3 (11 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1949 (Rfree = 0.000) for 1372 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1893 (Rfree = 0.000) for 1368 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 12 peptides. Score 0.374 Round 2: 107 peptides, 16 chains. Longest chain 16 peptides. Score 0.511 Round 3: 104 peptides, 15 chains. Longest chain 18 peptides. Score 0.520 Round 4: 101 peptides, 17 chains. Longest chain 16 peptides. Score 0.440 Round 5: 90 peptides, 15 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 3 Chains 16, Residues 89, Estimated correctness of the model 17.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 2912 restraints for refining 1373 atoms. 2526 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.1932 (Rfree = 0.000) for 1374 atoms. Found 6 (11 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1882 (Rfree = 0.000) for 1371 atoms. Found 7 (11 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.1839 (Rfree = 0.000) for 1371 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1900 (Rfree = 0.000) for 1364 atoms. Found 5 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.363 Round 2: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.392 Round 3: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.407 Round 4: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.372 Round 5: 72 peptides, 13 chains. Longest chain 15 peptides. Score 0.349 Taking the results from Round 3 Chains 15, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3403 reflections ( 97.79 % complete ) and 3156 restraints for refining 1373 atoms. 2879 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2030 (Rfree = 0.000) for 1373 atoms. Found 9 (11 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.1907 (Rfree = 0.000) for 1376 atoms. Found 7 (11 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1897 (Rfree = 0.000) for 1376 atoms. Found 5 (11 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1840 (Rfree = 0.000) for 1372 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1818 (Rfree = 0.000) for 1367 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 9 peptides. Score 0.268 Round 2: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.399 Round 3: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.386 Round 4: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.400 Round 5: 76 peptides, 12 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 64, 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 2pw4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3403 reflections ( 97.79 % complete ) and 3196 restraints for refining 1373 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2070 (Rfree = 0.000) for 1373 atoms. Found 0 (11 requested) and removed 3 (6 requested) atoms. Cycle 47: After refmac, R = 0.2064 (Rfree = 0.000) for 1368 atoms. Found 0 (11 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.1966 (Rfree = 0.000) for 1363 atoms. Found 0 (11 requested) and removed 3 (6 requested) atoms. Cycle 49: After refmac, R = 0.2203 (Rfree = 0.000) for 1360 atoms. Found 0 (11 requested) and removed 3 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:37 GMT 2018 Job finished. TimeTaking 28.59 Used memory is bytes: 22100976