Sun 23 Dec 22:23:10 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 2hdo-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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/2hdo-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 22:23:18 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/2hdo-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-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 131 and 0 Target number of residues in the AU: 131 Target solvent content: 0.6572 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 209 Adjusted target solvent content: 0.45 Input MTZ file: 2hdo-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: 169 Cell parameters: 87.040 87.040 47.290 90.000 90.000 120.000 Input sequence file: 2hdo-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1672 target number of atoms Had to go as low as 0.80 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: 29.474 3.802 Wilson plot Bfac: 81.90 2082 reflections ( 99.52 % complete ) and 0 restraints for refining 1853 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3379 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2994 (Rfree = 0.000) for 1853 atoms. Found 10 (10 requested) and removed 37 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.96 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.246 Round 2: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.356 Round 3: 113 peptides, 18 chains. Longest chain 14 peptides. Score 0.496 Round 4: 117 peptides, 19 chains. Longest chain 13 peptides. Score 0.494 Round 5: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 20, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 3430 restraints for refining 1509 atoms. 3034 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2477 (Rfree = 0.000) for 1509 atoms. Found 5 (8 requested) and removed 19 (4 requested) atoms. Cycle 2: After refmac, R = 0.2300 (Rfree = 0.000) for 1459 atoms. Found 2 (8 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2341 (Rfree = 0.000) for 1439 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 4: After refmac, R = 0.2176 (Rfree = 0.000) for 1423 atoms. Found 4 (7 requested) and removed 11 (3 requested) atoms. Cycle 5: After refmac, R = 0.2128 (Rfree = 0.000) for 1411 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 1493 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.379 Round 2: 120 peptides, 20 chains. Longest chain 14 peptides. Score 0.485 Round 3: 108 peptides, 18 chains. Longest chain 14 peptides. Score 0.461 Round 4: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.518 Round 5: 117 peptides, 19 chains. Longest chain 14 peptides. Score 0.494 Taking the results from Round 4 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 3339 restraints for refining 1492 atoms. 2944 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1993 (Rfree = 0.000) for 1492 atoms. Found 5 (8 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.1829 (Rfree = 0.000) for 1468 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.1886 (Rfree = 0.000) for 1456 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.1902 (Rfree = 0.000) for 1444 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1919 (Rfree = 0.000) for 1444 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.266 Round 2: 100 peptides, 18 chains. Longest chain 17 peptides. Score 0.402 Round 3: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.348 Round 4: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.420 Round 5: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.437 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 3495 restraints for refining 1512 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1917 (Rfree = 0.000) for 1512 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 12: After refmac, R = 0.1967 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 13: After refmac, R = 0.2193 (Rfree = 0.000) for 1469 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 14: After refmac, R = 0.1867 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.1642 (Rfree = 0.000) for 1445 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.250 Round 2: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.341 Round 3: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.379 Round 4: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.399 Round 5: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 4 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 3139 restraints for refining 1406 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1885 (Rfree = 0.000) for 1406 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 17: After refmac, R = 0.2035 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.1968 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.1762 (Rfree = 0.000) for 1386 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.1855 (Rfree = 0.000) for 1380 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 1465 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 10 peptides. Score 0.292 Round 2: 98 peptides, 17 chains. Longest chain 13 peptides. Score 0.420 Round 3: 107 peptides, 18 chains. Longest chain 15 peptides. Score 0.454 Round 4: 108 peptides, 19 chains. Longest chain 14 peptides. Score 0.430 Round 5: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 3 Chains 20, Residues 89, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 2969 restraints for refining 1423 atoms. 2600 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1973 (Rfree = 0.000) for 1423 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.1791 (Rfree = 0.000) for 1406 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.1767 (Rfree = 0.000) for 1400 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.1700 (Rfree = 0.000) for 1390 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1650 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.87 Search for helices and strands: 0 residues in 0 chains, 1471 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 5 peptides. Score 0.228 Round 2: 98 peptides, 20 chains. Longest chain 9 peptides. Score 0.321 Round 3: 91 peptides, 19 chains. Longest chain 6 peptides. Score 0.297 Round 4: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.314 Round 5: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 5 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 2957 restraints for refining 1392 atoms. 2648 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2033 (Rfree = 0.000) for 1392 atoms. Found 4 (7 requested) and removed 9 (3 requested) atoms. Cycle 27: After refmac, R = 0.2061 (Rfree = 0.000) for 1383 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.1875 (Rfree = 0.000) for 1379 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.1300 (Rfree = 0.000) for 1373 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1178 (Rfree = 0.000) for 1366 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 1423 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.254 Round 2: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.319 Round 3: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.351 Round 4: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.242 Round 5: 67 peptides, 14 chains. Longest chain 6 peptides. Score 0.270 Taking the results from Round 3 Chains 16, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 3002 restraints for refining 1385 atoms. 2742 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2174 (Rfree = 0.000) for 1385 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 32: After refmac, R = 0.2028 (Rfree = 0.000) for 1382 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.1928 (Rfree = 0.000) for 1377 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 34: After refmac, R = 0.1877 (Rfree = 0.000) for 1373 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.1780 (Rfree = 0.000) for 1368 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 1441 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.216 Round 2: 74 peptides, 16 chains. Longest chain 6 peptides. Score 0.258 Round 3: 80 peptides, 16 chains. Longest chain 7 peptides. Score 0.310 Round 4: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.372 Round 5: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.396 Taking the results from Round 5 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 2986 restraints for refining 1377 atoms. 2728 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2019 (Rfree = 0.000) for 1377 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.2119 (Rfree = 0.000) for 1368 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 38: After refmac, R = 0.1983 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.2018 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 1413 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.299 Round 2: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.364 Round 3: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.339 Round 4: 78 peptides, 13 chains. Longest chain 8 peptides. Score 0.399 Round 5: 71 peptides, 12 chains. Longest chain 7 peptides. Score 0.377 Taking the results from Round 4 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2082 reflections ( 99.52 % complete ) and 2987 restraints for refining 1363 atoms. 2740 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1917 (Rfree = 0.000) for 1363 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2082 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.1959 (Rfree = 0.000) for 1355 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.1943 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.1861 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.89 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.274 Round 2: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.322 Round 3: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.299 Round 4: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.288 Round 5: 69 peptides, 13 chains. Longest chain 7 peptides. Score 0.325 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 56, 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 2hdo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2082 reflections ( 99.52 % complete ) and 3070 restraints for refining 1386 atoms. 2859 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2031 (Rfree = 0.000) for 1386 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2002 (Rfree = 0.000) for 1374 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2031 (Rfree = 0.000) for 1365 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1839 (Rfree = 0.000) for 1358 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 29.05