Sun 23 Dec 22:22:41 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 2huh-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huh-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huh-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-1.5-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/2huh-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-1.5-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 22:22:50 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/2huh-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-1.5-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 152 and 0 Target number of residues in the AU: 152 Target solvent content: 0.4684 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 147 Adjusted target solvent content: 0.49 Input MTZ file: 2huh-1.5-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: 96 Cell parameters: 43.026 43.026 167.168 90.000 90.000 90.000 Input sequence file: 2huh-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1176 target number of atoms Had to go as low as 0.35 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 1 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: 41.792 1.540 Wilson plot Bfac: 17.33 23961 reflections ( 98.51 % complete ) and 0 restraints for refining 1298 atoms. Observations/parameters ratio is 4.61 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2828 (Rfree = 0.000) for 1298 atoms. Found 91 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.68 1.70 Round 1: 131 peptides, 4 chains. Longest chain 47 peptides. Score 0.927 Round 2: 139 peptides, 2 chains. Longest chain 74 peptides. Score 0.956 Round 3: 140 peptides, 1 chains. Longest chain 140 peptides. Score 0.965 Round 4: 139 peptides, 3 chains. Longest chain 115 peptides. Score 0.948 Round 5: 138 peptides, 4 chains. Longest chain 70 peptides. Score 0.937 Taking the results from Round 3 Chains 1, Residues 139, Estimated correctness of the model 99.9 % 1 chains (139 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1235 restraints for refining 1280 atoms. 90 conditional restraints added. Observations/parameters ratio is 4.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2610 (Rfree = 0.000) for 1280 atoms. Found 56 (92 requested) and removed 25 (46 requested) atoms. Cycle 2: After refmac, R = 0.2228 (Rfree = 0.000) for 1311 atoms. Found 55 (94 requested) and removed 17 (47 requested) atoms. Cycle 3: After refmac, R = 0.2098 (Rfree = 0.000) for 1347 atoms. Found 48 (97 requested) and removed 30 (48 requested) atoms. Cycle 4: After refmac, R = 0.2006 (Rfree = 0.000) for 1363 atoms. Found 56 (96 requested) and removed 11 (49 requested) atoms. Cycle 5: After refmac, R = 0.1960 (Rfree = 0.000) for 1407 atoms. Found 39 (99 requested) and removed 30 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 140 peptides, 2 chains. Longest chain 114 peptides. Score 0.957 Round 3: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 4: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 5: 140 peptides, 2 chains. Longest chain 77 peptides. Score 0.957 Taking the results from Round 3 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1270 restraints for refining 1339 atoms. 116 conditional restraints added. Observations/parameters ratio is 4.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2003 (Rfree = 0.000) for 1339 atoms. Found 76 (92 requested) and removed 24 (48 requested) atoms. Cycle 7: After refmac, R = 0.1971 (Rfree = 0.000) for 1391 atoms. Found 61 (96 requested) and removed 29 (50 requested) atoms. Cycle 8: After refmac, R = 0.1947 (Rfree = 0.000) for 1421 atoms. Found 51 (98 requested) and removed 34 (51 requested) atoms. Cycle 9: After refmac, R = 0.1951 (Rfree = 0.000) for 1436 atoms. Found 44 (97 requested) and removed 35 (51 requested) atoms. Cycle 10: After refmac, R = 0.1928 (Rfree = 0.000) for 1444 atoms. Found 43 (96 requested) and removed 34 (52 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 4: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 5: 140 peptides, 2 chains. Longest chain 77 peptides. Score 0.957 Taking the results from Round 3 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1290 restraints for refining 1357 atoms. 136 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1979 (Rfree = 0.000) for 1357 atoms. Found 87 (87 requested) and removed 16 (48 requested) atoms. Cycle 12: After refmac, R = 0.1977 (Rfree = 0.000) for 1427 atoms. Found 31 (93 requested) and removed 38 (51 requested) atoms. Cycle 13: After refmac, R = 0.1909 (Rfree = 0.000) for 1418 atoms. Found 46 (90 requested) and removed 21 (51 requested) atoms. Cycle 14: After refmac, R = 0.1894 (Rfree = 0.000) for 1441 atoms. Found 46 (92 requested) and removed 29 (52 requested) atoms. Cycle 15: After refmac, R = 0.1887 (Rfree = 0.000) for 1457 atoms. Found 43 (90 requested) and removed 30 (52 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 4: 140 peptides, 2 chains. Longest chain 114 peptides. Score 0.957 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1297 restraints for refining 1368 atoms. 143 conditional restraints added. Observations/parameters ratio is 4.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1951 (Rfree = 0.000) for 1368 atoms. Found 82 (82 requested) and removed 22 (49 requested) atoms. Cycle 17: After refmac, R = 0.1991 (Rfree = 0.000) for 1426 atoms. Found 46 (87 requested) and removed 35 (51 requested) atoms. Cycle 18: After refmac, R = 0.1937 (Rfree = 0.000) for 1434 atoms. Found 46 (84 requested) and removed 22 (51 requested) atoms. Cycle 19: After refmac, R = 0.1901 (Rfree = 0.000) for 1458 atoms. Found 37 (86 requested) and removed 39 (52 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 1452 atoms. Found 49 (84 requested) and removed 29 (52 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 4: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1305 restraints for refining 1376 atoms. 151 conditional restraints added. Observations/parameters ratio is 4.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1948 (Rfree = 0.000) for 1376 atoms. Found 77 (77 requested) and removed 23 (49 requested) atoms. Cycle 22: After refmac, R = 0.1978 (Rfree = 0.000) for 1428 atoms. Found 34 (80 requested) and removed 39 (51 requested) atoms. Cycle 23: After refmac, R = 0.1904 (Rfree = 0.000) for 1421 atoms. Found 50 (78 requested) and removed 19 (51 requested) atoms. Cycle 24: After refmac, R = 0.1900 (Rfree = 0.000) for 1451 atoms. Found 33 (79 requested) and removed 35 (52 requested) atoms. Cycle 25: After refmac, R = 0.1880 (Rfree = 0.000) for 1448 atoms. Found 45 (77 requested) and removed 33 (52 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 4: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 5: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Taking the results from Round 4 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1294 restraints for refining 1366 atoms. 140 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1977 (Rfree = 0.000) for 1366 atoms. Found 71 (71 requested) and removed 19 (49 requested) atoms. Cycle 27: After refmac, R = 0.1974 (Rfree = 0.000) for 1416 atoms. Found 41 (73 requested) and removed 25 (51 requested) atoms. Cycle 28: After refmac, R = 0.1918 (Rfree = 0.000) for 1431 atoms. Found 39 (72 requested) and removed 22 (51 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 1446 atoms. Found 35 (71 requested) and removed 22 (52 requested) atoms. Cycle 30: After refmac, R = 0.1922 (Rfree = 0.000) for 1457 atoms. Found 43 (69 requested) and removed 23 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.65 1.67 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 4: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 23961 reflections ( 98.51 % complete ) and 1298 restraints for refining 1362 atoms. 144 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1960 (Rfree = 0.000) for 1362 atoms. Found 63 (63 requested) and removed 19 (49 requested) atoms. Cycle 32: After refmac, R = 0.1966 (Rfree = 0.000) for 1404 atoms. Found 48 (65 requested) and removed 30 (50 requested) atoms. Cycle 33: After refmac, R = 0.1916 (Rfree = 0.000) for 1421 atoms. Found 53 (63 requested) and removed 27 (51 requested) atoms. Cycle 34: After refmac, R = 0.1931 (Rfree = 0.000) for 1446 atoms. Found 48 (62 requested) and removed 32 (52 requested) atoms. Cycle 35: After refmac, R = 0.1889 (Rfree = 0.000) for 1462 atoms. Found 48 (61 requested) and removed 32 (52 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 3: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 4: 139 peptides, 3 chains. Longest chain 64 peptides. Score 0.948 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1328 restraints for refining 1375 atoms. 174 conditional restraints added. Observations/parameters ratio is 4.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1978 (Rfree = 0.000) for 1375 atoms. Found 55 (55 requested) and removed 21 (49 requested) atoms. Cycle 37: After refmac, R = 0.1951 (Rfree = 0.000) for 1407 atoms. Found 56 (57 requested) and removed 20 (50 requested) atoms. Cycle 38: After refmac, R = 0.1935 (Rfree = 0.000) for 1440 atoms. Found 44 (58 requested) and removed 30 (52 requested) atoms. Cycle 39: After refmac, R = 0.1916 (Rfree = 0.000) for 1452 atoms. Found 48 (56 requested) and removed 21 (52 requested) atoms. Cycle 40: After refmac, R = 0.1898 (Rfree = 0.000) for 1477 atoms. Found 41 (57 requested) and removed 38 (53 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 3: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 4: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence ------------------------------------------------------ 23961 reflections ( 98.51 % complete ) and 1324 restraints for refining 1384 atoms. 170 conditional restraints added. Observations/parameters ratio is 4.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1977 (Rfree = 0.000) for 1384 atoms. Found 51 (51 requested) and removed 20 (49 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 1411 atoms. Found 53 (53 requested) and removed 22 (51 requested) atoms. Cycle 43: After refmac, R = 0.1932 (Rfree = 0.000) for 1442 atoms. Found 48 (54 requested) and removed 32 (52 requested) atoms. Cycle 44: After refmac, R = 0.1913 (Rfree = 0.000) for 1456 atoms. Found 48 (52 requested) and removed 38 (52 requested) atoms. Cycle 45: After refmac, R = 0.1911 (Rfree = 0.000) for 1463 atoms. Found 52 (52 requested) and removed 32 (52 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.64 1.66 Round 1: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 2: 140 peptides, 2 chains. Longest chain 122 peptides. Score 0.957 Round 3: 140 peptides, 2 chains. Longest chain 81 peptides. Score 0.957 Round 4: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Round 5: 141 peptides, 1 chains. Longest chain 141 peptides. Score 0.966 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 140, Estimated correctness of the model 99.9 % 1 chains (140 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23961 reflections ( 98.51 % complete ) and 1154 restraints for refining 1126 atoms. Observations/parameters ratio is 5.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2554 (Rfree = 0.000) for 1126 atoms. Found 40 (40 requested) and removed 0 (40 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2366 (Rfree = 0.000) for 1126 atoms. Found 28 (42 requested) and removed 0 (42 requested) atoms. Cycle 48: After refmac, R = 0.2199 (Rfree = 0.000) for 1126 atoms. Found 7 (43 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2116 (Rfree = 0.000) for 1126 atoms. Found 17 (43 requested) and removed 1 (43 requested) atoms. Writing output files ... TimeTaking 34.27