Mon 24 Dec 01:06:19 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obn-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:06:23 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/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-mrncs/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 807 and 0 Target number of residues in the AU: 807 Target solvent content: 0.6768 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-4.0-parrot-mrncs.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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.70 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 4.000 Wilson plot Bfac: 98.12 11286 reflections ( 99.58 % complete ) and 0 restraints for refining 12306 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3187 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3093 (Rfree = 0.000) for 12306 atoms. Found 58 (58 requested) and removed 79 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 4.23 Search for helices and strands: 0 residues in 0 chains, 12539 seeds are put forward NCS extension: 0 residues added, 12539 seeds are put forward Round 1: 382 peptides, 82 chains. Longest chain 11 peptides. Score 0.247 Round 2: 545 peptides, 104 chains. Longest chain 10 peptides. Score 0.341 Round 3: 608 peptides, 105 chains. Longest chain 21 peptides. Score 0.412 Round 4: 607 peptides, 104 chains. Longest chain 17 peptides. Score 0.416 Round 5: 652 peptides, 103 chains. Longest chain 22 peptides. Score 0.471 Taking the results from Round 5 Chains 103, Residues 549, Estimated correctness of the model 0.0 % 9 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23879 restraints for refining 10082 atoms. 21680 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2494 (Rfree = 0.000) for 10082 atoms. Found 36 (47 requested) and removed 67 (23 requested) atoms. Cycle 2: After refmac, R = 0.2237 (Rfree = 0.000) for 9875 atoms. Found 38 (47 requested) and removed 53 (23 requested) atoms. Cycle 3: After refmac, R = 0.1846 (Rfree = 0.000) for 9759 atoms. Found 18 (46 requested) and removed 46 (23 requested) atoms. Cycle 4: After refmac, R = 0.2227 (Rfree = 0.000) for 9664 atoms. Found 26 (46 requested) and removed 38 (23 requested) atoms. Cycle 5: After refmac, R = 0.2177 (Rfree = 0.000) for 9597 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 9919 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 9935 seeds are put forward Round 1: 481 peptides, 102 chains. Longest chain 11 peptides. Score 0.269 Round 2: 576 peptides, 99 chains. Longest chain 17 peptides. Score 0.405 Round 3: 586 peptides, 94 chains. Longest chain 16 peptides. Score 0.441 Round 4: 600 peptides, 96 chains. Longest chain 15 peptides. Score 0.447 Round 5: 597 peptides, 100 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 4 Chains 96, Residues 504, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22683 restraints for refining 9487 atoms. 20735 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 9487 atoms. Found 30 (45 requested) and removed 576 (22 requested) atoms. Cycle 7: After refmac, R = 0.2216 (Rfree = 0.000) for 8859 atoms. Found 42 (42 requested) and removed 50 (21 requested) atoms. Cycle 8: After refmac, R = 0.1721 (Rfree = 0.000) for 8776 atoms. Found 23 (42 requested) and removed 42 (21 requested) atoms. Cycle 9: After refmac, R = 0.1589 (Rfree = 0.000) for 8733 atoms. Found 13 (41 requested) and removed 32 (20 requested) atoms. Cycle 10: After refmac, R = 0.1563 (Rfree = 0.000) for 8691 atoms. Found 10 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 8999 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9017 seeds are put forward Round 1: 530 peptides, 108 chains. Longest chain 10 peptides. Score 0.301 Round 2: 595 peptides, 104 chains. Longest chain 19 peptides. Score 0.402 Round 3: 582 peptides, 95 chains. Longest chain 19 peptides. Score 0.432 Round 4: 621 peptides, 100 chains. Longest chain 18 peptides. Score 0.451 Round 5: 625 peptides, 101 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 5 Chains 104, Residues 524, Estimated correctness of the model 0.0 % 9 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 20839 restraints for refining 9264 atoms. 18683 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2056 (Rfree = 0.000) for 9264 atoms. Found 33 (44 requested) and removed 83 (22 requested) atoms. Cycle 12: After refmac, R = 0.2003 (Rfree = 0.000) for 9144 atoms. Found 40 (43 requested) and removed 47 (21 requested) atoms. Cycle 13: After refmac, R = 0.1830 (Rfree = 0.000) for 9102 atoms. Found 25 (43 requested) and removed 36 (21 requested) atoms. Cycle 14: After refmac, R = 0.1440 (Rfree = 0.000) for 9057 atoms. Found 12 (43 requested) and removed 37 (21 requested) atoms. Cycle 15: After refmac, R = 0.1372 (Rfree = 0.000) for 9009 atoms. Found 7 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.87 4.19 Search for helices and strands: 0 residues in 0 chains, 9328 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 9345 seeds are put forward Round 1: 537 peptides, 106 chains. Longest chain 12 peptides. Score 0.320 Round 2: 607 peptides, 102 chains. Longest chain 18 peptides. Score 0.426 Round 3: 628 peptides, 103 chains. Longest chain 16 peptides. Score 0.445 Round 4: 616 peptides, 102 chains. Longest chain 14 peptides. Score 0.436 Round 5: 605 peptides, 89 chains. Longest chain 20 peptides. Score 0.486 Taking the results from Round 5 Chains 92, Residues 516, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22268 restraints for refining 9718 atoms. 20146 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1864 (Rfree = 0.000) for 9718 atoms. Found 33 (46 requested) and removed 82 (23 requested) atoms. Cycle 17: After refmac, R = 0.1751 (Rfree = 0.000) for 9600 atoms. Found 31 (45 requested) and removed 51 (22 requested) atoms. Cycle 18: After refmac, R = 0.1748 (Rfree = 0.000) for 9545 atoms. Found 29 (45 requested) and removed 41 (22 requested) atoms. Cycle 19: After refmac, R = 0.1677 (Rfree = 0.000) for 9503 atoms. Found 25 (45 requested) and removed 39 (22 requested) atoms. Cycle 20: After refmac, R = 0.1295 (Rfree = 0.000) for 9460 atoms. Found 8 (45 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 9730 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 9748 seeds are put forward Round 1: 471 peptides, 95 chains. Longest chain 11 peptides. Score 0.295 Round 2: 501 peptides, 89 chains. Longest chain 18 peptides. Score 0.366 Round 3: 547 peptides, 92 chains. Longest chain 14 peptides. Score 0.406 Round 4: 554 peptides, 92 chains. Longest chain 18 peptides. Score 0.414 Round 5: 546 peptides, 95 chains. Longest chain 15 peptides. Score 0.389 Taking the results from Round 4 Chains 92, Residues 462, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 23157 restraints for refining 9770 atoms. 21365 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1777 (Rfree = 0.000) for 9770 atoms. Found 17 (46 requested) and removed 72 (23 requested) atoms. Cycle 22: After refmac, R = 0.1858 (Rfree = 0.000) for 9664 atoms. Found 35 (46 requested) and removed 58 (23 requested) atoms. Cycle 23: After refmac, R = 0.1679 (Rfree = 0.000) for 9606 atoms. Found 26 (45 requested) and removed 52 (22 requested) atoms. Cycle 24: After refmac, R = 0.1713 (Rfree = 0.000) for 9549 atoms. Found 36 (45 requested) and removed 36 (22 requested) atoms. Cycle 25: After refmac, R = 0.1583 (Rfree = 0.000) for 9514 atoms. Found 39 (45 requested) and removed 39 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 9822 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 9839 seeds are put forward Round 1: 432 peptides, 90 chains. Longest chain 14 peptides. Score 0.271 Round 2: 467 peptides, 85 chains. Longest chain 21 peptides. Score 0.345 Round 3: 477 peptides, 85 chains. Longest chain 11 peptides. Score 0.358 Round 4: 473 peptides, 79 chains. Longest chain 13 peptides. Score 0.385 Round 5: 483 peptides, 84 chains. Longest chain 19 peptides. Score 0.371 Taking the results from Round 4 Chains 79, Residues 394, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22733 restraints for refining 9577 atoms. 21194 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2053 (Rfree = 0.000) for 9577 atoms. Found 45 (45 requested) and removed 48 (22 requested) atoms. Cycle 27: After refmac, R = 0.1871 (Rfree = 0.000) for 9515 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 28: After refmac, R = 0.1404 (Rfree = 0.000) for 9477 atoms. Found 14 (45 requested) and removed 30 (22 requested) atoms. Cycle 29: After refmac, R = 0.1275 (Rfree = 0.000) for 9440 atoms. Found 14 (44 requested) and removed 30 (22 requested) atoms. Cycle 30: After refmac, R = 0.1242 (Rfree = 0.000) for 9412 atoms. Found 10 (44 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.87 4.19 Search for helices and strands: 0 residues in 0 chains, 9636 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 9651 seeds are put forward Round 1: 408 peptides, 91 chains. Longest chain 9 peptides. Score 0.231 Round 2: 462 peptides, 88 chains. Longest chain 13 peptides. Score 0.322 Round 3: 471 peptides, 89 chains. Longest chain 17 peptides. Score 0.328 Round 4: 433 peptides, 77 chains. Longest chain 25 peptides. Score 0.346 Round 5: 463 peptides, 80 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 5 Chains 80, Residues 383, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22608 restraints for refining 9520 atoms. 21129 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 9520 atoms. Found 45 (45 requested) and removed 59 (22 requested) atoms. Cycle 32: After refmac, R = 0.1890 (Rfree = 0.000) for 9465 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 33: After refmac, R = 0.1807 (Rfree = 0.000) for 9424 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 34: After refmac, R = 0.1731 (Rfree = 0.000) for 9395 atoms. Found 39 (44 requested) and removed 37 (22 requested) atoms. Cycle 35: After refmac, R = 0.1870 (Rfree = 0.000) for 9362 atoms. Found 44 (44 requested) and removed 31 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 9620 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 9638 seeds are put forward Round 1: 324 peptides, 72 chains. Longest chain 11 peptides. Score 0.223 Round 2: 396 peptides, 84 chains. Longest chain 11 peptides. Score 0.255 Round 3: 392 peptides, 75 chains. Longest chain 10 peptides. Score 0.303 Round 4: 397 peptides, 75 chains. Longest chain 10 peptides. Score 0.309 Round 5: 407 peptides, 79 chains. Longest chain 11 peptides. Score 0.300 Taking the results from Round 4 Chains 75, Residues 322, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22338 restraints for refining 9342 atoms. 21080 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2008 (Rfree = 0.000) for 9342 atoms. Found 44 (44 requested) and removed 53 (22 requested) atoms. Cycle 37: After refmac, R = 0.1736 (Rfree = 0.000) for 9297 atoms. Found 36 (44 requested) and removed 43 (22 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 9271 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 9253 atoms. Found 36 (44 requested) and removed 32 (22 requested) atoms. Cycle 40: After refmac, R = 0.1369 (Rfree = 0.000) for 9242 atoms. Found 7 (43 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 4.18 Search for helices and strands: 0 residues in 0 chains, 9484 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 9496 seeds are put forward Round 1: 329 peptides, 71 chains. Longest chain 10 peptides. Score 0.237 Round 2: 377 peptides, 76 chains. Longest chain 9 peptides. Score 0.276 Round 3: 368 peptides, 69 chains. Longest chain 12 peptides. Score 0.305 Round 4: 380 peptides, 72 chains. Longest chain 13 peptides. Score 0.304 Round 5: 397 peptides, 74 chains. Longest chain 12 peptides. Score 0.315 Taking the results from Round 5 Chains 74, Residues 323, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 21752 restraints for refining 9236 atoms. 20534 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2098 (Rfree = 0.000) for 9236 atoms. Found 43 (43 requested) and removed 65 (21 requested) atoms. Cycle 42: After refmac, R = 0.1891 (Rfree = 0.000) for 9171 atoms. Found 43 (43 requested) and removed 41 (21 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 9147 atoms. Found 43 (43 requested) and removed 41 (21 requested) atoms. Cycle 44: After refmac, R = 0.1893 (Rfree = 0.000) for 9120 atoms. Found 43 (43 requested) and removed 39 (21 requested) atoms. Cycle 45: After refmac, R = 0.1274 (Rfree = 0.000) for 9095 atoms. Found 16 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 4.18 Search for helices and strands: 0 residues in 0 chains, 9351 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 9368 seeds are put forward Round 1: 294 peptides, 66 chains. Longest chain 8 peptides. Score 0.215 Round 2: 357 peptides, 72 chains. Longest chain 9 peptides. Score 0.272 Round 3: 347 peptides, 68 chains. Longest chain 10 peptides. Score 0.282 Round 4: 356 peptides, 69 chains. Longest chain 11 peptides. Score 0.289 Round 5: 380 peptides, 70 chains. Longest chain 12 peptides. Score 0.316 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 310, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2obn-4_warpNtrace.pdb as input Building loops using Loopy2018 71 chains (310 residues) following loop building 4 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11286 reflections ( 99.58 % complete ) and 21182 restraints for refining 9070 atoms. 19966 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2016 (Rfree = 0.000) for 9070 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1877 (Rfree = 0.000) for 9010 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1815 (Rfree = 0.000) for 8966 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 8913 atoms. TimeTaking 83.23