Mon 24 Dec 01:12:14 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 1vrb-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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/1vrb-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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 01:12:18 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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 896 and 0 Target number of residues in the AU: 896 Target solvent content: 0.6580 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.6-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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: 48.979 3.600 Wilson plot Bfac: 83.52 17139 reflections ( 98.80 % complete ) and 0 restraints for refining 12069 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3193 (Rfree = 0.000) for 12069 atoms. Found 77 (77 requested) and removed 189 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 12184 seeds are put forward NCS extension: 0 residues added, 12184 seeds are put forward Round 1: 473 peptides, 96 chains. Longest chain 15 peptides. Score 0.287 Round 2: 589 peptides, 100 chains. Longest chain 13 peptides. Score 0.406 Round 3: 603 peptides, 97 chains. Longest chain 20 peptides. Score 0.436 Round 4: 653 peptides, 101 chains. Longest chain 12 peptides. Score 0.471 Round 5: 676 peptides, 101 chains. Longest chain 23 peptides. Score 0.494 Taking the results from Round 5 Chains 102, Residues 575, Estimated correctness of the model 0.0 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22647 restraints for refining 9916 atoms. 20208 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2562 (Rfree = 0.000) for 9916 atoms. Found 49 (63 requested) and removed 115 (31 requested) atoms. Cycle 2: After refmac, R = 0.2451 (Rfree = 0.000) for 9696 atoms. Found 34 (63 requested) and removed 62 (31 requested) atoms. Cycle 3: After refmac, R = 0.2395 (Rfree = 0.000) for 9595 atoms. Found 36 (62 requested) and removed 56 (31 requested) atoms. Cycle 4: After refmac, R = 0.2330 (Rfree = 0.000) for 9531 atoms. Found 38 (61 requested) and removed 53 (30 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2141 (Rfree = 0.000) for 9475 atoms. Found 18 (61 requested) and removed 49 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 9775 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 9789 seeds are put forward Round 1: 570 peptides, 110 chains. Longest chain 12 peptides. Score 0.334 Round 2: 681 peptides, 106 chains. Longest chain 20 peptides. Score 0.477 Round 3: 664 peptides, 102 chains. Longest chain 22 peptides. Score 0.477 Round 4: 705 peptides, 108 chains. Longest chain 32 peptides. Score 0.492 Round 5: 693 peptides, 104 chains. Longest chain 23 peptides. Score 0.498 Taking the results from Round 5 Chains 104, Residues 589, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22263 restraints for refining 9791 atoms. 19939 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2417 (Rfree = 0.000) for 9791 atoms. Found 51 (62 requested) and removed 121 (31 requested) atoms. Cycle 7: After refmac, R = 0.2314 (Rfree = 0.000) for 9633 atoms. Found 59 (62 requested) and removed 74 (31 requested) atoms. Cycle 8: After refmac, R = 0.2017 (Rfree = 0.000) for 9563 atoms. Found 20 (61 requested) and removed 43 (30 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1959 (Rfree = 0.000) for 9506 atoms. Found 11 (61 requested) and removed 38 (30 requested) atoms. Cycle 10: After refmac, R = 0.1930 (Rfree = 0.000) for 9462 atoms. Found 15 (60 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.57 Search for helices and strands: 0 residues in 0 chains, 9755 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 9794 seeds are put forward Round 1: 552 peptides, 107 chains. Longest chain 15 peptides. Score 0.328 Round 2: 637 peptides, 109 chains. Longest chain 15 peptides. Score 0.416 Round 3: 646 peptides, 105 chains. Longest chain 19 peptides. Score 0.445 Round 4: 630 peptides, 98 chains. Longest chain 18 peptides. Score 0.460 Round 5: 648 peptides, 100 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 5 Chains 100, Residues 548, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22314 restraints for refining 9730 atoms. 20151 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2385 (Rfree = 0.000) for 9730 atoms. Found 54 (62 requested) and removed 96 (31 requested) atoms. Cycle 12: After refmac, R = 0.2267 (Rfree = 0.000) for 9627 atoms. Found 53 (62 requested) and removed 57 (31 requested) atoms. Cycle 13: After refmac, R = 0.2293 (Rfree = 0.000) for 9576 atoms. Found 55 (61 requested) and removed 63 (30 requested) atoms. Cycle 14: After refmac, R = 0.2227 (Rfree = 0.000) for 9520 atoms. Found 54 (61 requested) and removed 57 (30 requested) atoms. Cycle 15: After refmac, R = 0.2233 (Rfree = 0.000) for 9488 atoms. Found 61 (61 requested) and removed 55 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 9891 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 9925 seeds are put forward Round 1: 482 peptides, 100 chains. Longest chain 10 peptides. Score 0.278 Round 2: 567 peptides, 105 chains. Longest chain 18 peptides. Score 0.356 Round 3: 576 peptides, 103 chains. Longest chain 17 peptides. Score 0.377 Round 4: 567 peptides, 95 chains. Longest chain 17 peptides. Score 0.406 Round 5: 579 peptides, 95 chains. Longest chain 17 peptides. Score 0.419 Taking the results from Round 5 Chains 95, Residues 484, Estimated correctness of the model 0.0 % 8 chains (33 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22689 restraints for refining 9802 atoms. 20767 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2390 (Rfree = 0.000) for 9802 atoms. Found 62 (62 requested) and removed 112 (31 requested) atoms. Cycle 17: After refmac, R = 0.2244 (Rfree = 0.000) for 9699 atoms. Found 62 (62 requested) and removed 59 (31 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1989 (Rfree = 0.000) for 9664 atoms. Found 18 (62 requested) and removed 44 (31 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 9612 atoms. Found 18 (61 requested) and removed 38 (30 requested) atoms. Cycle 20: After refmac, R = 0.1934 (Rfree = 0.000) for 9580 atoms. Found 20 (61 requested) and removed 46 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 9853 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 9886 seeds are put forward Round 1: 454 peptides, 97 chains. Longest chain 9 peptides. Score 0.257 Round 2: 542 peptides, 102 chains. Longest chain 11 peptides. Score 0.341 Round 3: 578 peptides, 100 chains. Longest chain 16 peptides. Score 0.394 Round 4: 557 peptides, 94 chains. Longest chain 14 peptides. Score 0.399 Round 5: 571 peptides, 99 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 94, Residues 463, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23267 restraints for refining 9875 atoms. 21490 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2328 (Rfree = 0.000) for 9875 atoms. Found 63 (63 requested) and removed 102 (31 requested) atoms. Cycle 22: After refmac, R = 0.2255 (Rfree = 0.000) for 9780 atoms. Found 63 (63 requested) and removed 61 (31 requested) atoms. Cycle 23: After refmac, R = 0.2235 (Rfree = 0.000) for 9753 atoms. Found 62 (62 requested) and removed 68 (31 requested) atoms. Cycle 24: After refmac, R = 0.1909 (Rfree = 0.000) for 9710 atoms. Found 19 (62 requested) and removed 46 (31 requested) atoms. Cycle 25: After refmac, R = 0.1824 (Rfree = 0.000) for 9664 atoms. Found 19 (62 requested) and removed 40 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 9950 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 9963 seeds are put forward Round 1: 407 peptides, 90 chains. Longest chain 8 peptides. Score 0.233 Round 2: 471 peptides, 88 chains. Longest chain 13 peptides. Score 0.328 Round 3: 475 peptides, 88 chains. Longest chain 14 peptides. Score 0.333 Round 4: 495 peptides, 84 chains. Longest chain 14 peptides. Score 0.378 Round 5: 494 peptides, 91 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 4 Chains 85, Residues 411, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22744 restraints for refining 9730 atoms. 21125 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2192 (Rfree = 0.000) for 9730 atoms. Found 53 (62 requested) and removed 74 (31 requested) atoms. Cycle 27: After refmac, R = 0.2172 (Rfree = 0.000) for 9673 atoms. Found 62 (62 requested) and removed 57 (31 requested) atoms. Cycle 28: After refmac, R = 0.2146 (Rfree = 0.000) for 9638 atoms. Found 62 (62 requested) and removed 51 (31 requested) atoms. Cycle 29: After refmac, R = 0.1920 (Rfree = 0.000) for 9616 atoms. Found 17 (61 requested) and removed 34 (30 requested) atoms. Cycle 30: After refmac, R = 0.1880 (Rfree = 0.000) for 9573 atoms. Found 13 (61 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 9796 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 9812 seeds are put forward Round 1: 349 peptides, 72 chains. Longest chain 11 peptides. Score 0.257 Round 2: 415 peptides, 78 chains. Longest chain 13 peptides. Score 0.311 Round 3: 417 peptides, 73 chains. Longest chain 13 peptides. Score 0.341 Round 4: 429 peptides, 75 chains. Longest chain 12 peptides. Score 0.345 Round 5: 446 peptides, 76 chains. Longest chain 19 peptides. Score 0.361 Taking the results from Round 5 Chains 76, Residues 370, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22626 restraints for refining 9676 atoms. 21123 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2259 (Rfree = 0.000) for 9676 atoms. Found 51 (62 requested) and removed 83 (31 requested) atoms. Cycle 32: After refmac, R = 0.2254 (Rfree = 0.000) for 9601 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. Cycle 33: After refmac, R = 0.2320 (Rfree = 0.000) for 9562 atoms. Found 61 (61 requested) and removed 62 (30 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 9530 atoms. Found 17 (61 requested) and removed 43 (30 requested) atoms. Cycle 35: After refmac, R = 0.1865 (Rfree = 0.000) for 9476 atoms. Found 18 (60 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 9709 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 9740 seeds are put forward Round 1: 337 peptides, 73 chains. Longest chain 8 peptides. Score 0.234 Round 2: 411 peptides, 79 chains. Longest chain 9 peptides. Score 0.301 Round 3: 414 peptides, 73 chains. Longest chain 16 peptides. Score 0.338 Round 4: 405 peptides, 75 chains. Longest chain 10 peptides. Score 0.315 Round 5: 404 peptides, 71 chains. Longest chain 13 peptides. Score 0.336 Taking the results from Round 3 Chains 73, Residues 341, Estimated correctness of the model 0.0 % 7 chains (26 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21684 restraints for refining 9418 atoms. 20332 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2314 (Rfree = 0.000) for 9418 atoms. Found 60 (60 requested) and removed 65 (30 requested) atoms. Cycle 37: After refmac, R = 0.2337 (Rfree = 0.000) for 9388 atoms. Found 60 (60 requested) and removed 55 (30 requested) atoms. Cycle 38: After refmac, R = 0.2411 (Rfree = 0.000) for 9364 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 39: After refmac, R = 0.2361 (Rfree = 0.000) for 9347 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 9344 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 9597 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 9616 seeds are put forward Round 1: 294 peptides, 66 chains. Longest chain 7 peptides. Score 0.214 Round 2: 385 peptides, 75 chains. Longest chain 10 peptides. Score 0.289 Round 3: 373 peptides, 71 chains. Longest chain 10 peptides. Score 0.296 Round 4: 376 peptides, 70 chains. Longest chain 9 peptides. Score 0.306 Round 5: 371 peptides, 69 chains. Longest chain 11 peptides. Score 0.305 Taking the results from Round 4 Chains 70, Residues 306, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21313 restraints for refining 9277 atoms. 20088 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2408 (Rfree = 0.000) for 9277 atoms. Found 59 (59 requested) and removed 59 (29 requested) atoms. Cycle 42: After refmac, R = 0.2327 (Rfree = 0.000) for 9251 atoms. Found 59 (59 requested) and removed 44 (29 requested) atoms. Cycle 43: After refmac, R = 0.2298 (Rfree = 0.000) for 9244 atoms. Found 59 (59 requested) and removed 52 (29 requested) atoms. Cycle 44: After refmac, R = 0.2258 (Rfree = 0.000) for 9227 atoms. Found 59 (59 requested) and removed 35 (29 requested) atoms. Cycle 45: After refmac, R = 0.1948 (Rfree = 0.000) for 9232 atoms. Found 24 (59 requested) and removed 34 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 9478 seeds are put forward NCS extension: 0 residues added, 9478 seeds are put forward Round 1: 333 peptides, 76 chains. Longest chain 7 peptides. Score 0.210 Round 2: 393 peptides, 79 chains. Longest chain 9 peptides. Score 0.277 Round 3: 403 peptides, 77 chains. Longest chain 11 peptides. Score 0.301 Round 4: 412 peptides, 81 chains. Longest chain 11 peptides. Score 0.291 Round 5: 413 peptides, 75 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 338, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 139 B and 146 B 74 chains (344 residues) following loop building 4 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17139 reflections ( 98.80 % complete ) and 21259 restraints for refining 9331 atoms. 19896 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2161 (Rfree = 0.000) for 9331 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 9261 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2178 (Rfree = 0.000) for 9200 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.2138 (Rfree = 0.000) for 9142 atoms. TimeTaking 89.38