null Tue 25 Dec 19:27:55 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 2obn-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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/2obn-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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 ============================================================ Tue 25 Dec 19:28:05 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/2obn-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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 836 and 0 Target number of residues in the AU: 836 Target solvent content: 0.6652 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 11168 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 73.214 3.800 Wilson plot Bfac: 88.54 13122 reflections ( 99.61 % complete ) and 0 restraints for refining 12319 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3109 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3009 (Rfree = 0.000) for 12319 atoms. Found 67 (67 requested) and removed 92 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 12526 seeds are put forward NCS extension: 0 residues added, 12526 seeds are put forward Round 1: 441 peptides, 90 chains. Longest chain 12 peptides. Score 0.283 Round 2: 581 peptides, 106 chains. Longest chain 16 peptides. Score 0.375 Round 3: 652 peptides, 107 chains. Longest chain 17 peptides. Score 0.452 Round 4: 681 peptides, 106 chains. Longest chain 14 peptides. Score 0.488 Round 5: 693 peptides, 105 chains. Longest chain 13 peptides. Score 0.505 Taking the results from Round 5 Chains 105, Residues 588, Estimated correctness of the model 0.0 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23348 restraints for refining 10100 atoms. 20905 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2303 (Rfree = 0.000) for 10100 atoms. Found 43 (55 requested) and removed 77 (27 requested) atoms. Cycle 2: After refmac, R = 0.2122 (Rfree = 0.000) for 9892 atoms. Found 29 (55 requested) and removed 52 (27 requested) atoms. Cycle 3: After refmac, R = 0.2064 (Rfree = 0.000) for 9775 atoms. Found 20 (54 requested) and removed 47 (27 requested) atoms. Cycle 4: After refmac, R = 0.1995 (Rfree = 0.000) for 9695 atoms. Found 26 (53 requested) and removed 39 (26 requested) atoms. Cycle 5: After refmac, R = 0.1970 (Rfree = 0.000) for 9638 atoms. Found 28 (53 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 9944 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 9955 seeds are put forward Round 1: 528 peptides, 102 chains. Longest chain 12 peptides. Score 0.330 Round 2: 636 peptides, 111 chains. Longest chain 14 peptides. Score 0.415 Round 3: 708 peptides, 118 chains. Longest chain 14 peptides. Score 0.461 Round 4: 660 peptides, 104 chains. Longest chain 22 peptides. Score 0.475 Round 5: 669 peptides, 104 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 105, Residues 565, Estimated correctness of the model 0.0 % 10 chains (55 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 21842 restraints for refining 9520 atoms. 19542 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2294 (Rfree = 0.000) for 9520 atoms. Found 52 (52 requested) and removed 66 (26 requested) atoms. Cycle 7: After refmac, R = 0.2188 (Rfree = 0.000) for 9414 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 8: After refmac, R = 0.2025 (Rfree = 0.000) for 9355 atoms. Found 26 (51 requested) and removed 46 (25 requested) atoms. Cycle 9: After refmac, R = 0.1878 (Rfree = 0.000) for 9276 atoms. Found 30 (51 requested) and removed 40 (25 requested) atoms. Cycle 10: After refmac, R = 0.1887 (Rfree = 0.000) for 9230 atoms. Found 32 (50 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 9571 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 9589 seeds are put forward Round 1: 521 peptides, 104 chains. Longest chain 11 peptides. Score 0.311 Round 2: 607 peptides, 104 chains. Longest chain 13 peptides. Score 0.416 Round 3: 643 peptides, 109 chains. Longest chain 19 peptides. Score 0.432 Round 4: 607 peptides, 91 chains. Longest chain 16 peptides. Score 0.479 Round 5: 645 peptides, 100 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 4 Chains 94, Residues 516, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 21764 restraints for refining 9475 atoms. 19692 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2111 (Rfree = 0.000) for 9475 atoms. Found 51 (52 requested) and removed 60 (26 requested) atoms. Cycle 12: After refmac, R = 0.1972 (Rfree = 0.000) for 9395 atoms. Found 52 (52 requested) and removed 47 (26 requested) atoms. Cycle 13: After refmac, R = 0.1894 (Rfree = 0.000) for 9357 atoms. Found 47 (51 requested) and removed 40 (25 requested) atoms. Cycle 14: After refmac, R = 0.1878 (Rfree = 0.000) for 9333 atoms. Found 48 (51 requested) and removed 35 (25 requested) atoms. Cycle 15: After refmac, R = 0.1816 (Rfree = 0.000) for 9315 atoms. Found 30 (51 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 9641 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 9656 seeds are put forward Round 1: 493 peptides, 97 chains. Longest chain 12 peptides. Score 0.312 Round 2: 599 peptides, 100 chains. Longest chain 18 peptides. Score 0.426 Round 3: 614 peptides, 100 chains. Longest chain 14 peptides. Score 0.443 Round 4: 593 peptides, 91 chains. Longest chain 15 peptides. Score 0.464 Round 5: 614 peptides, 97 chains. Longest chain 18 peptides. Score 0.458 Taking the results from Round 4 Chains 92, Residues 502, Estimated correctness of the model 0.0 % 7 chains (44 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 22527 restraints for refining 9696 atoms. 20476 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1983 (Rfree = 0.000) for 9696 atoms. Found 34 (53 requested) and removed 69 (26 requested) atoms. Cycle 17: After refmac, R = 0.1802 (Rfree = 0.000) for 9606 atoms. Found 32 (53 requested) and removed 48 (26 requested) atoms. Cycle 18: After refmac, R = 0.1759 (Rfree = 0.000) for 9569 atoms. Found 27 (52 requested) and removed 39 (26 requested) atoms. Cycle 19: After refmac, R = 0.1747 (Rfree = 0.000) for 9539 atoms. Found 31 (52 requested) and removed 44 (26 requested) atoms. Cycle 20: After refmac, R = 0.1668 (Rfree = 0.000) for 9514 atoms. Found 31 (52 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 9818 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9831 seeds are put forward Round 1: 512 peptides, 104 chains. Longest chain 11 peptides. Score 0.299 Round 2: 587 peptides, 102 chains. Longest chain 14 peptides. Score 0.402 Round 3: 600 peptides, 101 chains. Longest chain 15 peptides. Score 0.423 Round 4: 618 peptides, 98 chains. Longest chain 19 peptides. Score 0.457 Round 5: 624 peptides, 99 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 5 Chains 102, Residues 525, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23242 restraints for refining 10101 atoms. 21090 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1837 (Rfree = 0.000) for 10101 atoms. Found 23 (55 requested) and removed 80 (27 requested) atoms. Cycle 22: After refmac, R = 0.1735 (Rfree = 0.000) for 9982 atoms. Found 33 (55 requested) and removed 62 (27 requested) atoms. Cycle 23: After refmac, R = 0.1665 (Rfree = 0.000) for 9924 atoms. Found 32 (54 requested) and removed 34 (27 requested) atoms. Cycle 24: After refmac, R = 0.1650 (Rfree = 0.000) for 9896 atoms. Found 37 (54 requested) and removed 39 (27 requested) atoms. Cycle 25: After refmac, R = 0.1665 (Rfree = 0.000) for 9875 atoms. Found 42 (54 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 10208 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10227 seeds are put forward Round 1: 463 peptides, 98 chains. Longest chain 10 peptides. Score 0.267 Round 2: 545 peptides, 98 chains. Longest chain 14 peptides. Score 0.373 Round 3: 565 peptides, 99 chains. Longest chain 16 peptides. Score 0.392 Round 4: 564 peptides, 96 chains. Longest chain 13 peptides. Score 0.406 Round 5: 585 peptides, 97 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 98, Residues 488, Estimated correctness of the model 0.0 % 11 chains (48 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 23602 restraints for refining 10097 atoms. 21638 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1857 (Rfree = 0.000) for 10097 atoms. Found 46 (55 requested) and removed 67 (27 requested) atoms. Cycle 27: After refmac, R = 0.1747 (Rfree = 0.000) for 10007 atoms. Found 44 (55 requested) and removed 44 (27 requested) atoms. Cycle 28: After refmac, R = 0.1674 (Rfree = 0.000) for 9975 atoms. Found 36 (55 requested) and removed 46 (27 requested) atoms. Cycle 29: After refmac, R = 0.1610 (Rfree = 0.000) for 9939 atoms. Found 35 (54 requested) and removed 37 (27 requested) atoms. Cycle 30: After refmac, R = 0.1243 (Rfree = 0.000) for 9922 atoms. Found 4 (54 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 10205 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 10228 seeds are put forward Round 1: 411 peptides, 92 chains. Longest chain 7 peptides. Score 0.230 Round 2: 482 peptides, 88 chains. Longest chain 16 peptides. Score 0.348 Round 3: 487 peptides, 88 chains. Longest chain 13 peptides. Score 0.354 Round 4: 492 peptides, 85 chains. Longest chain 14 peptides. Score 0.376 Round 5: 491 peptides, 81 chains. Longest chain 17 peptides. Score 0.396 Taking the results from Round 5 Chains 83, Residues 410, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24160 restraints for refining 10101 atoms. 22523 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1813 (Rfree = 0.000) for 10101 atoms. Found 45 (55 requested) and removed 42 (27 requested) atoms. Cycle 32: After refmac, R = 0.1864 (Rfree = 0.000) for 10058 atoms. Found 55 (55 requested) and removed 43 (27 requested) atoms. Cycle 33: After refmac, R = 0.1775 (Rfree = 0.000) for 10033 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. Cycle 34: After refmac, R = 0.1702 (Rfree = 0.000) for 10021 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. Cycle 35: After refmac, R = 0.1646 (Rfree = 0.000) for 10022 atoms. Found 40 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 10324 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 10342 seeds are put forward Round 1: 369 peptides, 83 chains. Longest chain 9 peptides. Score 0.223 Round 2: 422 peptides, 81 chains. Longest chain 13 peptides. Score 0.308 Round 3: 435 peptides, 79 chains. Longest chain 15 peptides. Score 0.337 Round 4: 428 peptides, 76 chains. Longest chain 10 peptides. Score 0.345 Round 5: 429 peptides, 78 chains. Longest chain 14 peptides. Score 0.335 Taking the results from Round 4 Chains 76, Residues 352, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24347 restraints for refining 10101 atoms. 22958 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1738 (Rfree = 0.000) for 10101 atoms. Found 40 (55 requested) and removed 52 (27 requested) atoms. Cycle 37: After refmac, R = 0.1679 (Rfree = 0.000) for 10048 atoms. Found 55 (55 requested) and removed 48 (27 requested) atoms. Cycle 38: After refmac, R = 0.1630 (Rfree = 0.000) for 10037 atoms. Found 49 (55 requested) and removed 39 (27 requested) atoms. Cycle 39: After refmac, R = 0.1159 (Rfree = 0.000) for 10037 atoms. Found 6 (55 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.1045 (Rfree = 0.000) for 10001 atoms. Found 7 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 10257 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 10269 seeds are put forward Round 1: 372 peptides, 81 chains. Longest chain 8 peptides. Score 0.239 Round 2: 447 peptides, 86 chains. Longest chain 12 peptides. Score 0.313 Round 3: 457 peptides, 87 chains. Longest chain 10 peptides. Score 0.321 Round 4: 449 peptides, 87 chains. Longest chain 11 peptides. Score 0.310 Round 5: 445 peptides, 84 chains. Longest chain 12 peptides. Score 0.322 Taking the results from Round 5 Chains 84, Residues 361, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 13122 reflections ( 99.61 % complete ) and 24614 restraints for refining 10100 atoms. 23237 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1720 (Rfree = 0.000) for 10100 atoms. Found 47 (55 requested) and removed 41 (27 requested) atoms. Cycle 42: After refmac, R = 0.1666 (Rfree = 0.000) for 10072 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 43: After refmac, R = 0.1635 (Rfree = 0.000) for 10064 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. Cycle 44: After refmac, R = 0.1105 (Rfree = 0.000) for 10066 atoms. Found 13 (55 requested) and removed 29 (27 requested) atoms. Cycle 45: After refmac, R = 0.0984 (Rfree = 0.000) for 10039 atoms. Found 7 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 10286 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 10298 seeds are put forward Round 1: 359 peptides, 83 chains. Longest chain 7 peptides. Score 0.208 Round 2: 413 peptides, 83 chains. Longest chain 11 peptides. Score 0.285 Round 3: 397 peptides, 79 chains. Longest chain 9 peptides. Score 0.286 Round 4: 405 peptides, 77 chains. Longest chain 11 peptides. Score 0.309 Round 5: 422 peptides, 79 chains. Longest chain 10 peptides. Score 0.320 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 343, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 79 chains (343 residues) following loop building 6 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13122 reflections ( 99.61 % complete ) and 24229 restraints for refining 10099 atoms. 22894 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1553 (Rfree = 0.000) for 10099 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1621 (Rfree = 0.000) for 10040 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 10001 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1526 (Rfree = 0.000) for 9950 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:33:38 GMT 2018 Job finished. TimeTaking 125.71 Used memory is bytes: 8774608