Mon 24 Dec 00:43:18 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 1vr0-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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/1vr0-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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 00:43:22 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/1vr0-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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 523 and 0 Target number of residues in the AU: 523 Target solvent content: 0.6136 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.2-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.200 Wilson plot Bfac: 58.25 12698 reflections ( 99.73 % complete ) and 0 restraints for refining 6594 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3120 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2447 (Rfree = 0.000) for 6594 atoms. Found 38 (59 requested) and removed 114 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 3.27 Search for helices and strands: 0 residues in 0 chains, 6659 seeds are put forward NCS extension: 0 residues added, 6659 seeds are put forward Round 1: 380 peptides, 68 chains. Longest chain 14 peptides. Score 0.419 Round 2: 425 peptides, 55 chains. Longest chain 27 peptides. Score 0.606 Round 3: 466 peptides, 57 chains. Longest chain 19 peptides. Score 0.654 Round 4: 485 peptides, 56 chains. Longest chain 21 peptides. Score 0.686 Round 5: 507 peptides, 57 chains. Longest chain 34 peptides. Score 0.708 Taking the results from Round 5 Chains 58, Residues 450, Estimated correctness of the model 66.9 % 3 chains (57 residues) have been docked in sequence Building loops using Loopy2018 58 chains (450 residues) following loop building 3 chains (57 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11122 restraints for refining 5411 atoms. 9139 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2538 (Rfree = 0.000) for 5411 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 2: After refmac, R = 0.2297 (Rfree = 0.000) for 5362 atoms. Found 21 (47 requested) and removed 34 (24 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 5317 atoms. Found 11 (45 requested) and removed 24 (23 requested) atoms. Cycle 4: After refmac, R = 0.2135 (Rfree = 0.000) for 5290 atoms. Found 8 (44 requested) and removed 24 (23 requested) atoms. Cycle 5: After refmac, R = 0.2128 (Rfree = 0.000) for 5264 atoms. Found 10 (43 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 5462 seeds are put forward NCS extension: 14 residues added (15 deleted due to clashes), 5476 seeds are put forward Round 1: 445 peptides, 54 chains. Longest chain 34 peptides. Score 0.643 Round 2: 497 peptides, 52 chains. Longest chain 35 peptides. Score 0.724 Round 3: 506 peptides, 50 chains. Longest chain 36 peptides. Score 0.745 Round 4: 500 peptides, 48 chains. Longest chain 36 peptides. Score 0.748 Round 5: 519 peptides, 51 chains. Longest chain 36 peptides. Score 0.753 Taking the results from Round 5 Chains 54, Residues 468, Estimated correctness of the model 75.6 % 6 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 118 A 52 chains (470 residues) following loop building 5 chains (111 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 10664 restraints for refining 5412 atoms. 8435 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2549 (Rfree = 0.000) for 5412 atoms. Found 32 (43 requested) and removed 39 (24 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 5379 atoms. Found 13 (42 requested) and removed 27 (24 requested) atoms. Cycle 8: After refmac, R = 0.2156 (Rfree = 0.000) for 5351 atoms. Found 4 (41 requested) and removed 27 (24 requested) atoms. Cycle 9: After refmac, R = 0.2067 (Rfree = 0.000) for 5317 atoms. Found 2 (39 requested) and removed 27 (23 requested) atoms. Cycle 10: After refmac, R = 0.2069 (Rfree = 0.000) for 5286 atoms. Found 8 (39 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 5462 seeds are put forward NCS extension: 4 residues added (10 deleted due to clashes), 5466 seeds are put forward Round 1: 439 peptides, 57 chains. Longest chain 23 peptides. Score 0.614 Round 2: 484 peptides, 55 chains. Longest chain 25 peptides. Score 0.691 Round 3: 486 peptides, 54 chains. Longest chain 35 peptides. Score 0.699 Round 4: 504 peptides, 55 chains. Longest chain 40 peptides. Score 0.716 Round 5: 484 peptides, 55 chains. Longest chain 39 peptides. Score 0.691 Taking the results from Round 4 Chains 57, Residues 449, Estimated correctness of the model 68.5 % 5 chains (107 residues) have been docked in sequence Building loops using Loopy2018 57 chains (449 residues) following loop building 5 chains (107 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 10831 restraints for refining 5412 atoms. 8688 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2375 (Rfree = 0.000) for 5412 atoms. Found 38 (38 requested) and removed 39 (24 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 5397 atoms. Found 15 (37 requested) and removed 27 (24 requested) atoms. Cycle 13: After refmac, R = 0.2116 (Rfree = 0.000) for 5373 atoms. Found 11 (36 requested) and removed 25 (24 requested) atoms. Cycle 14: After refmac, R = 0.2225 (Rfree = 0.000) for 5357 atoms. Found 19 (36 requested) and removed 26 (24 requested) atoms. Cycle 15: After refmac, R = 0.2035 (Rfree = 0.000) for 5343 atoms. Found 8 (35 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 5518 seeds are put forward NCS extension: 22 residues added (28 deleted due to clashes), 5540 seeds are put forward Round 1: 439 peptides, 51 chains. Longest chain 27 peptides. Score 0.655 Round 2: 491 peptides, 57 chains. Longest chain 23 peptides. Score 0.688 Round 3: 506 peptides, 48 chains. Longest chain 45 peptides. Score 0.755 Round 4: 486 peptides, 53 chains. Longest chain 24 peptides. Score 0.705 Round 5: 486 peptides, 56 chains. Longest chain 25 peptides. Score 0.688 Taking the results from Round 3 Chains 50, Residues 458, Estimated correctness of the model 76.0 % 5 chains (135 residues) have been docked in sequence Building loops using Loopy2018 50 chains (458 residues) following loop building 5 chains (135 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 10470 restraints for refining 5412 atoms. 8196 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2332 (Rfree = 0.000) for 5412 atoms. Found 34 (34 requested) and removed 39 (24 requested) atoms. Cycle 17: After refmac, R = 0.2289 (Rfree = 0.000) for 5395 atoms. Found 23 (33 requested) and removed 33 (24 requested) atoms. Cycle 18: After refmac, R = 0.2237 (Rfree = 0.000) for 5373 atoms. Found 21 (32 requested) and removed 28 (24 requested) atoms. Cycle 19: After refmac, R = 0.2030 (Rfree = 0.000) for 5349 atoms. Found 15 (31 requested) and removed 28 (24 requested) atoms. Cycle 20: After refmac, R = 0.1921 (Rfree = 0.000) for 5327 atoms. Found 10 (29 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 5491 seeds are put forward NCS extension: 41 residues added (9 deleted due to clashes), 5532 seeds are put forward Round 1: 417 peptides, 54 chains. Longest chain 35 peptides. Score 0.600 Round 2: 460 peptides, 56 chains. Longest chain 26 peptides. Score 0.652 Round 3: 463 peptides, 54 chains. Longest chain 21 peptides. Score 0.669 Round 4: 465 peptides, 54 chains. Longest chain 24 peptides. Score 0.672 Round 5: 444 peptides, 50 chains. Longest chain 31 peptides. Score 0.668 Taking the results from Round 4 Chains 56, Residues 411, Estimated correctness of the model 59.0 % 6 chains (92 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11159 restraints for refining 5412 atoms. 9222 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2261 (Rfree = 0.000) for 5412 atoms. Found 29 (29 requested) and removed 34 (24 requested) atoms. Cycle 22: After refmac, R = 0.2064 (Rfree = 0.000) for 5394 atoms. Found 23 (29 requested) and removed 25 (24 requested) atoms. Cycle 23: After refmac, R = 0.1971 (Rfree = 0.000) for 5388 atoms. Found 13 (29 requested) and removed 25 (24 requested) atoms. Cycle 24: After refmac, R = 0.1934 (Rfree = 0.000) for 5375 atoms. Found 9 (29 requested) and removed 24 (24 requested) atoms. Cycle 25: After refmac, R = 0.1820 (Rfree = 0.000) for 5358 atoms. Found 5 (29 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 5523 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 5553 seeds are put forward Round 1: 419 peptides, 57 chains. Longest chain 20 peptides. Score 0.582 Round 2: 453 peptides, 52 chains. Longest chain 23 peptides. Score 0.668 Round 3: 465 peptides, 48 chains. Longest chain 28 peptides. Score 0.708 Round 4: 446 peptides, 49 chains. Longest chain 21 peptides. Score 0.677 Round 5: 438 peptides, 49 chains. Longest chain 36 peptides. Score 0.666 Taking the results from Round 3 Chains 49, Residues 417, Estimated correctness of the model 66.9 % 5 chains (66 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 80 A 48 chains (420 residues) following loop building 4 chains (71 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11300 restraints for refining 5412 atoms. 9448 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2223 (Rfree = 0.000) for 5412 atoms. Found 29 (29 requested) and removed 39 (24 requested) atoms. Cycle 27: After refmac, R = 0.1975 (Rfree = 0.000) for 5390 atoms. Found 16 (28 requested) and removed 27 (24 requested) atoms. Cycle 28: After refmac, R = 0.2209 (Rfree = 0.000) for 5368 atoms. Found 27 (27 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.1865 (Rfree = 0.000) for 5361 atoms. Found 10 (26 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.1860 (Rfree = 0.000) for 5343 atoms. Found 19 (24 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 5519 seeds are put forward NCS extension: 25 residues added (21 deleted due to clashes), 5544 seeds are put forward Round 1: 382 peptides, 51 chains. Longest chain 29 peptides. Score 0.564 Round 2: 428 peptides, 50 chains. Longest chain 31 peptides. Score 0.645 Round 3: 425 peptides, 50 chains. Longest chain 28 peptides. Score 0.641 Round 4: 427 peptides, 53 chains. Longest chain 26 peptides. Score 0.623 Round 5: 414 peptides, 49 chains. Longest chain 33 peptides. Score 0.631 Taking the results from Round 2 Chains 51, Residues 378, Estimated correctness of the model 52.6 % 5 chains (88 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11363 restraints for refining 5412 atoms. 9611 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2050 (Rfree = 0.000) for 5412 atoms. Found 24 (24 requested) and removed 34 (24 requested) atoms. Cycle 32: After refmac, R = 0.2070 (Rfree = 0.000) for 5393 atoms. Found 17 (24 requested) and removed 27 (24 requested) atoms. Cycle 33: After refmac, R = 0.2317 (Rfree = 0.000) for 5377 atoms. Found 24 (24 requested) and removed 27 (24 requested) atoms. Cycle 34: After refmac, R = 0.2234 (Rfree = 0.000) for 5362 atoms. Found 24 (24 requested) and removed 27 (24 requested) atoms. Cycle 35: After refmac, R = 0.1828 (Rfree = 0.000) for 5352 atoms. Found 22 (24 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5528 seeds are put forward NCS extension: 23 residues added (28 deleted due to clashes), 5551 seeds are put forward Round 1: 383 peptides, 59 chains. Longest chain 21 peptides. Score 0.502 Round 2: 419 peptides, 51 chains. Longest chain 31 peptides. Score 0.625 Round 3: 414 peptides, 48 chains. Longest chain 28 peptides. Score 0.638 Round 4: 410 peptides, 46 chains. Longest chain 31 peptides. Score 0.646 Round 5: 400 peptides, 53 chains. Longest chain 22 peptides. Score 0.580 Taking the results from Round 4 Chains 48, Residues 364, Estimated correctness of the model 52.9 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11211 restraints for refining 5411 atoms. 9526 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2047 (Rfree = 0.000) for 5411 atoms. Found 24 (24 requested) and removed 36 (24 requested) atoms. Cycle 37: After refmac, R = 0.1943 (Rfree = 0.000) for 5392 atoms. Found 15 (24 requested) and removed 26 (24 requested) atoms. Cycle 38: After refmac, R = 0.2010 (Rfree = 0.000) for 5378 atoms. Found 23 (24 requested) and removed 26 (24 requested) atoms. Cycle 39: After refmac, R = 0.1842 (Rfree = 0.000) for 5370 atoms. Found 18 (24 requested) and removed 26 (24 requested) atoms. Cycle 40: After refmac, R = 0.1847 (Rfree = 0.000) for 5360 atoms. Found 15 (24 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5522 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 5538 seeds are put forward Round 1: 350 peptides, 50 chains. Longest chain 17 peptides. Score 0.514 Round 2: 400 peptides, 48 chains. Longest chain 25 peptides. Score 0.616 Round 3: 396 peptides, 48 chains. Longest chain 22 peptides. Score 0.610 Round 4: 394 peptides, 46 chains. Longest chain 22 peptides. Score 0.621 Round 5: 389 peptides, 47 chains. Longest chain 23 peptides. Score 0.606 Taking the results from Round 4 Chains 52, Residues 348, Estimated correctness of the model 46.6 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12698 reflections ( 99.73 % complete ) and 11555 restraints for refining 5412 atoms. 9962 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1985 (Rfree = 0.000) for 5412 atoms. Found 24 (24 requested) and removed 38 (24 requested) atoms. Cycle 42: After refmac, R = 0.1836 (Rfree = 0.000) for 5387 atoms. Found 19 (24 requested) and removed 26 (24 requested) atoms. Cycle 43: After refmac, R = 0.1786 (Rfree = 0.000) for 5374 atoms. Found 7 (24 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.1791 (Rfree = 0.000) for 5356 atoms. Found 7 (24 requested) and removed 25 (24 requested) atoms. Cycle 45: After refmac, R = 0.1767 (Rfree = 0.000) for 5336 atoms. Found 11 (23 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 5454 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5467 seeds are put forward Round 1: 328 peptides, 47 chains. Longest chain 25 peptides. Score 0.497 Round 2: 358 peptides, 45 chains. Longest chain 28 peptides. Score 0.569 Round 3: 357 peptides, 45 chains. Longest chain 18 peptides. Score 0.568 Round 4: 352 peptides, 45 chains. Longest chain 28 peptides. Score 0.559 Round 5: 354 peptides, 49 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 313, Estimated correctness of the model 32.4 % 3 chains (43 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input Building loops using Loopy2018 47 chains (313 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12698 reflections ( 99.73 % complete ) and 11938 restraints for refining 5412 atoms. 10581 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1922 (Rfree = 0.000) for 5412 atoms. Found 0 (24 requested) and removed 13 (24 requested) atoms. Cycle 47: After refmac, R = 0.1898 (Rfree = 0.000) for 5394 atoms. Found 0 (24 requested) and removed 7 (24 requested) atoms. Cycle 48: After refmac, R = 0.1866 (Rfree = 0.000) for 5386 atoms. Found 0 (24 requested) and removed 2 (24 requested) atoms. Cycle 49: After refmac, R = 0.1829 (Rfree = 0.000) for 5383 atoms. TimeTaking 62.02