Sun 23 Dec 22:22:53 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 2hyt-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hyt-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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/2hyt-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 22:23:03 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/2hyt-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hyt-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6693 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 197 Adjusted target solvent content: 0.52 Input MTZ file: 2hyt-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: 150 Cell parameters: 82.957 82.957 56.010 90.000 90.000 120.000 Input sequence file: 2hyt-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1576 target number of atoms Had to go as low as 0.90 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: 71.843 4.000 Wilson plot Bfac: 90.36 2013 reflections ( 99.41 % complete ) and 0 restraints for refining 1738 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3566 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3482 (Rfree = 0.000) for 1738 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 7 peptides. Score 0.289 Round 2: 58 peptides, 9 chains. Longest chain 12 peptides. Score 0.369 Round 3: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.382 Round 4: 84 peptides, 12 chains. Longest chain 14 peptides. Score 0.461 Round 5: 73 peptides, 10 chains. Longest chain 13 peptides. Score 0.448 Taking the results from Round 4 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3036 restraints for refining 1282 atoms. 2760 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3178 (Rfree = 0.000) for 1282 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 2: After refmac, R = 0.2943 (Rfree = 0.000) for 1261 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2533 (Rfree = 0.000) for 1246 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2104 (Rfree = 0.000) for 1241 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2070 (Rfree = 0.000) for 1237 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward Round 1: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.416 Round 2: 89 peptides, 12 chains. Longest chain 12 peptides. Score 0.494 Round 3: 92 peptides, 12 chains. Longest chain 20 peptides. Score 0.514 Round 4: 88 peptides, 12 chains. Longest chain 13 peptides. Score 0.488 Round 5: 96 peptides, 11 chains. Longest chain 13 peptides. Score 0.566 Taking the results from Round 5 Chains 11, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3200 restraints for refining 1371 atoms. 2871 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2440 (Rfree = 0.000) for 1371 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2410 (Rfree = 0.000) for 1348 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.2357 (Rfree = 0.000) for 1341 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2266 (Rfree = 0.000) for 1336 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2104 (Rfree = 0.000) for 1334 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 1405 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 6 peptides. Score 0.286 Round 2: 86 peptides, 14 chains. Longest chain 9 peptides. Score 0.413 Round 3: 86 peptides, 11 chains. Longest chain 22 peptides. Score 0.505 Round 4: 84 peptides, 11 chains. Longest chain 12 peptides. Score 0.492 Round 5: 83 peptides, 10 chains. Longest chain 13 peptides. Score 0.515 Taking the results from Round 5 Chains 10, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3314 restraints for refining 1392 atoms. 3032 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2580 (Rfree = 0.000) for 1392 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 1372 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2319 (Rfree = 0.000) for 1355 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2344 (Rfree = 0.000) for 1331 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.2140 (Rfree = 0.000) for 1321 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 7 peptides. Score 0.308 Round 2: 79 peptides, 15 chains. Longest chain 7 peptides. Score 0.328 Round 3: 87 peptides, 13 chains. Longest chain 11 peptides. Score 0.451 Round 4: 82 peptides, 10 chains. Longest chain 13 peptides. Score 0.509 Round 5: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 4 Chains 10, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3161 restraints for refining 1390 atoms. 2883 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2175 (Rfree = 0.000) for 1390 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2074 (Rfree = 0.000) for 1381 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.2137 (Rfree = 0.000) for 1373 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.1899 (Rfree = 0.000) for 1362 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1973 (Rfree = 0.000) for 1358 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.311 Round 2: 75 peptides, 10 chains. Longest chain 11 peptides. Score 0.462 Round 3: 75 peptides, 10 chains. Longest chain 16 peptides. Score 0.462 Round 4: 78 peptides, 10 chains. Longest chain 13 peptides. Score 0.482 Round 5: 82 peptides, 10 chains. Longest chain 16 peptides. Score 0.509 Taking the results from Round 5 Chains 10, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3261 restraints for refining 1423 atoms. 2983 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1990 (Rfree = 0.000) for 1423 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.1996 (Rfree = 0.000) for 1420 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2019 (Rfree = 0.000) for 1416 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.1697 (Rfree = 0.000) for 1412 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1764 (Rfree = 0.000) for 1408 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 14 peptides. Score 0.341 Round 2: 70 peptides, 9 chains. Longest chain 14 peptides. Score 0.459 Round 3: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.422 Round 4: 77 peptides, 9 chains. Longest chain 15 peptides. Score 0.506 Round 5: 74 peptides, 10 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 4 Chains 9, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3259 restraints for refining 1411 atoms. 2996 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2196 (Rfree = 0.000) for 1411 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2096 (Rfree = 0.000) for 1403 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.1925 (Rfree = 0.000) for 1401 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1769 (Rfree = 0.000) for 1399 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1637 (Rfree = 0.000) for 1396 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 1454 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 9 peptides. Score 0.298 Round 2: 80 peptides, 11 chains. Longest chain 16 peptides. Score 0.465 Round 3: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.426 Round 4: 81 peptides, 13 chains. Longest chain 13 peptides. Score 0.408 Round 5: 81 peptides, 13 chains. Longest chain 10 peptides. Score 0.408 Taking the results from Round 2 Chains 11, Residues 69, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3020 restraints for refining 1423 atoms. 2701 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1999 (Rfree = 0.000) for 1423 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.1790 (Rfree = 0.000) for 1412 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.1801 (Rfree = 0.000) for 1410 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1667 (Rfree = 0.000) for 1407 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1656 (Rfree = 0.000) for 1403 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1483 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 8 peptides. Score 0.239 Round 2: 77 peptides, 11 chains. Longest chain 12 peptides. Score 0.444 Round 3: 80 peptides, 11 chains. Longest chain 13 peptides. Score 0.465 Round 4: 74 peptides, 10 chains. Longest chain 15 peptides. Score 0.455 Round 5: 71 peptides, 9 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 9, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3362 restraints for refining 1423 atoms. 3123 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 1423 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.1928 (Rfree = 0.000) for 1418 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1627 (Rfree = 0.000) for 1419 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1634 (Rfree = 0.000) for 1419 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1603 (Rfree = 0.000) for 1417 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 9 peptides. Score 0.300 Round 2: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.411 Round 3: 65 peptides, 9 chains. Longest chain 15 peptides. Score 0.423 Round 4: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.346 Round 5: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 3 Chains 9, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2013 reflections ( 99.41 % complete ) and 3479 restraints for refining 1422 atoms. 3264 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2016 (Rfree = 0.000) for 1422 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 1418 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1758 (Rfree = 0.000) for 1417 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.1518 (Rfree = 0.000) for 1416 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.1667 (Rfree = 0.000) for 1413 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 1462 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.262 Round 2: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.349 Round 3: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.346 Round 4: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.429 Round 5: 64 peptides, 9 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, 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 2hyt-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2013 reflections ( 99.41 % complete ) and 3397 restraints for refining 1423 atoms. 3152 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2530 (Rfree = 0.000) for 1423 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2078 (Rfree = 0.000) for 1410 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1885 (Rfree = 0.000) for 1403 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1984 (Rfree = 0.000) for 1396 atoms. TimeTaking 30.43