Sun 23 Dec 23:55:36 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 1vl5-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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/1vl5-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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 ============================================================ Sun 23 Dec 23:55:40 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/1vl5-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.8-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 753 and 0 Target number of residues in the AU: 753 Target solvent content: 0.6482 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.8-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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.75 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: 49.849 3.800 Wilson plot Bfac: 76.86 11385 reflections ( 99.89 % complete ) and 0 restraints for refining 9280 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3241 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 9280 atoms. Found 51 (51 requested) and removed 65 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 9441 seeds are put forward NCS extension: 0 residues added, 9441 seeds are put forward Round 1: 413 peptides, 77 chains. Longest chain 12 peptides. Score 0.337 Round 2: 513 peptides, 76 chains. Longest chain 20 peptides. Score 0.481 Round 3: 543 peptides, 77 chains. Longest chain 25 peptides. Score 0.513 Round 4: 563 peptides, 76 chains. Longest chain 22 peptides. Score 0.541 Round 5: 579 peptides, 71 chains. Longest chain 27 peptides. Score 0.584 Taking the results from Round 5 Chains 75, Residues 508, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17172 restraints for refining 7522 atoms. 15078 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2294 (Rfree = 0.000) for 7522 atoms. Found 20 (41 requested) and removed 56 (20 requested) atoms. Cycle 2: After refmac, R = 0.2060 (Rfree = 0.000) for 7345 atoms. Found 14 (41 requested) and removed 37 (20 requested) atoms. Cycle 3: After refmac, R = 0.2069 (Rfree = 0.000) for 7257 atoms. Found 16 (40 requested) and removed 40 (20 requested) atoms. Cycle 4: After refmac, R = 0.1963 (Rfree = 0.000) for 7180 atoms. Found 20 (39 requested) and removed 28 (19 requested) atoms. Cycle 5: After refmac, R = 0.1933 (Rfree = 0.000) for 7136 atoms. Found 11 (39 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 7420 seeds are put forward NCS extension: 37 residues added (9 deleted due to clashes), 7457 seeds are put forward Round 1: 456 peptides, 78 chains. Longest chain 15 peptides. Score 0.393 Round 2: 528 peptides, 75 chains. Longest chain 23 peptides. Score 0.505 Round 3: 523 peptides, 69 chains. Longest chain 20 peptides. Score 0.531 Round 4: 536 peptides, 70 chains. Longest chain 20 peptides. Score 0.541 Round 5: 529 peptides, 70 chains. Longest chain 31 peptides. Score 0.533 Taking the results from Round 4 Chains 74, Residues 466, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 16342 restraints for refining 7333 atoms. 14378 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2135 (Rfree = 0.000) for 7333 atoms. Found 24 (40 requested) and removed 57 (20 requested) atoms. Cycle 7: After refmac, R = 0.1973 (Rfree = 0.000) for 7250 atoms. Found 9 (40 requested) and removed 36 (20 requested) atoms. Cycle 8: After refmac, R = 0.1973 (Rfree = 0.000) for 7209 atoms. Found 9 (39 requested) and removed 22 (19 requested) atoms. Cycle 9: After refmac, R = 0.1947 (Rfree = 0.000) for 7192 atoms. Found 5 (39 requested) and removed 23 (19 requested) atoms. Cycle 10: After refmac, R = 0.1928 (Rfree = 0.000) for 7173 atoms. Found 6 (39 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 7418 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7435 seeds are put forward Round 1: 508 peptides, 84 chains. Longest chain 18 peptides. Score 0.429 Round 2: 545 peptides, 72 chains. Longest chain 21 peptides. Score 0.541 Round 3: 562 peptides, 77 chains. Longest chain 18 peptides. Score 0.535 Round 4: 570 peptides, 73 chains. Longest chain 25 peptides. Score 0.565 Round 5: 567 peptides, 75 chains. Longest chain 23 peptides. Score 0.551 Taking the results from Round 4 Chains 74, Residues 497, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 16890 restraints for refining 7449 atoms. 14868 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2337 (Rfree = 0.000) for 7449 atoms. Found 24 (40 requested) and removed 71 (20 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 7349 atoms. Found 10 (40 requested) and removed 56 (20 requested) atoms. Cycle 13: After refmac, R = 0.1984 (Rfree = 0.000) for 7277 atoms. Found 17 (40 requested) and removed 41 (20 requested) atoms. Cycle 14: After refmac, R = 0.1948 (Rfree = 0.000) for 7225 atoms. Found 24 (39 requested) and removed 32 (19 requested) atoms. Cycle 15: After refmac, R = 0.1838 (Rfree = 0.000) for 7197 atoms. Found 12 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 7486 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 7517 seeds are put forward Round 1: 436 peptides, 80 chains. Longest chain 11 peptides. Score 0.352 Round 2: 547 peptides, 80 chains. Longest chain 18 peptides. Score 0.501 Round 3: 553 peptides, 76 chains. Longest chain 16 peptides. Score 0.530 Round 4: 528 peptides, 74 chains. Longest chain 17 peptides. Score 0.511 Round 5: 560 peptides, 77 chains. Longest chain 18 peptides. Score 0.533 Taking the results from Round 5 Chains 77, Residues 483, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17213 restraints for refining 7525 atoms. 15315 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2142 (Rfree = 0.000) for 7525 atoms. Found 27 (41 requested) and removed 54 (20 requested) atoms. Cycle 17: After refmac, R = 0.2031 (Rfree = 0.000) for 7429 atoms. Found 25 (41 requested) and removed 42 (20 requested) atoms. Cycle 18: After refmac, R = 0.1985 (Rfree = 0.000) for 7388 atoms. Found 34 (40 requested) and removed 49 (20 requested) atoms. Cycle 19: After refmac, R = 0.1887 (Rfree = 0.000) for 7356 atoms. Found 30 (40 requested) and removed 29 (20 requested) atoms. Cycle 20: After refmac, R = 0.1875 (Rfree = 0.000) for 7339 atoms. Found 20 (40 requested) and removed 40 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 7593 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7609 seeds are put forward Round 1: 435 peptides, 82 chains. Longest chain 15 peptides. Score 0.338 Round 2: 467 peptides, 75 chains. Longest chain 15 peptides. Score 0.427 Round 3: 491 peptides, 72 chains. Longest chain 18 peptides. Score 0.476 Round 4: 516 peptides, 76 chains. Longest chain 19 peptides. Score 0.485 Round 5: 511 peptides, 79 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 4 Chains 77, Residues 440, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17277 restraints for refining 7524 atoms. 15494 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2018 (Rfree = 0.000) for 7524 atoms. Found 32 (41 requested) and removed 42 (20 requested) atoms. Cycle 22: After refmac, R = 0.2038 (Rfree = 0.000) for 7451 atoms. Found 26 (41 requested) and removed 36 (20 requested) atoms. Cycle 23: After refmac, R = 0.1990 (Rfree = 0.000) for 7413 atoms. Found 27 (40 requested) and removed 38 (20 requested) atoms. Cycle 24: After refmac, R = 0.1928 (Rfree = 0.000) for 7372 atoms. Found 38 (40 requested) and removed 31 (20 requested) atoms. Cycle 25: After refmac, R = 0.1573 (Rfree = 0.000) for 7355 atoms. Found 7 (40 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 7592 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7609 seeds are put forward Round 1: 405 peptides, 77 chains. Longest chain 12 peptides. Score 0.325 Round 2: 475 peptides, 81 chains. Longest chain 13 peptides. Score 0.402 Round 3: 494 peptides, 80 chains. Longest chain 15 peptides. Score 0.434 Round 4: 495 peptides, 81 chains. Longest chain 14 peptides. Score 0.429 Round 5: 472 peptides, 71 chains. Longest chain 19 peptides. Score 0.457 Taking the results from Round 5 Chains 71, Residues 401, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17927 restraints for refining 7523 atoms. 16375 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2211 (Rfree = 0.000) for 7523 atoms. Found 40 (41 requested) and removed 51 (20 requested) atoms. Cycle 27: After refmac, R = 0.2025 (Rfree = 0.000) for 7468 atoms. Found 31 (41 requested) and removed 48 (20 requested) atoms. Cycle 28: After refmac, R = 0.1924 (Rfree = 0.000) for 7420 atoms. Found 31 (40 requested) and removed 38 (20 requested) atoms. Cycle 29: After refmac, R = 0.1869 (Rfree = 0.000) for 7394 atoms. Found 16 (40 requested) and removed 33 (20 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 7364 atoms. Found 29 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 7624 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7638 seeds are put forward Round 1: 397 peptides, 76 chains. Longest chain 10 peptides. Score 0.320 Round 2: 443 peptides, 72 chains. Longest chain 16 peptides. Score 0.412 Round 3: 467 peptides, 77 chains. Longest chain 17 peptides. Score 0.415 Round 4: 449 peptides, 69 chains. Longest chain 20 peptides. Score 0.438 Round 5: 442 peptides, 71 chains. Longest chain 14 peptides. Score 0.416 Taking the results from Round 4 Chains 70, Residues 380, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17711 restraints for refining 7523 atoms. 16212 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2070 (Rfree = 0.000) for 7523 atoms. Found 35 (41 requested) and removed 50 (20 requested) atoms. Cycle 32: After refmac, R = 0.2093 (Rfree = 0.000) for 7470 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 33: After refmac, R = 0.1940 (Rfree = 0.000) for 7445 atoms. Found 33 (41 requested) and removed 31 (20 requested) atoms. Cycle 34: After refmac, R = 0.1586 (Rfree = 0.000) for 7421 atoms. Found 17 (40 requested) and removed 29 (20 requested) atoms. Cycle 35: After refmac, R = 0.1546 (Rfree = 0.000) for 7391 atoms. Found 7 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 7597 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7613 seeds are put forward Round 1: 367 peptides, 73 chains. Longest chain 10 peptides. Score 0.293 Round 2: 440 peptides, 76 chains. Longest chain 12 peptides. Score 0.383 Round 3: 435 peptides, 72 chains. Longest chain 13 peptides. Score 0.401 Round 4: 442 peptides, 72 chains. Longest chain 16 peptides. Score 0.410 Round 5: 447 peptides, 72 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 5 Chains 72, Residues 375, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 17821 restraints for refining 7525 atoms. 16317 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2233 (Rfree = 0.000) for 7525 atoms. Found 41 (41 requested) and removed 48 (20 requested) atoms. Cycle 37: After refmac, R = 0.2077 (Rfree = 0.000) for 7461 atoms. Found 41 (41 requested) and removed 38 (20 requested) atoms. Cycle 38: After refmac, R = 0.1998 (Rfree = 0.000) for 7436 atoms. Found 40 (41 requested) and removed 34 (20 requested) atoms. Cycle 39: After refmac, R = 0.1967 (Rfree = 0.000) for 7407 atoms. Found 34 (40 requested) and removed 23 (20 requested) atoms. Cycle 40: After refmac, R = 0.1947 (Rfree = 0.000) for 7398 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 7665 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7679 seeds are put forward Round 1: 354 peptides, 73 chains. Longest chain 12 peptides. Score 0.272 Round 2: 428 peptides, 76 chains. Longest chain 15 peptides. Score 0.366 Round 3: 436 peptides, 73 chains. Longest chain 19 peptides. Score 0.396 Round 4: 428 peptides, 74 chains. Longest chain 13 peptides. Score 0.378 Round 5: 429 peptides, 68 chains. Longest chain 18 peptides. Score 0.417 Taking the results from Round 5 Chains 69, Residues 361, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11385 reflections ( 99.89 % complete ) and 18012 restraints for refining 7525 atoms. 16599 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2250 (Rfree = 0.000) for 7525 atoms. Found 41 (41 requested) and removed 46 (20 requested) atoms. Cycle 42: After refmac, R = 0.2084 (Rfree = 0.000) for 7473 atoms. Found 38 (41 requested) and removed 38 (20 requested) atoms. Cycle 43: After refmac, R = 0.2137 (Rfree = 0.000) for 7433 atoms. Found 41 (41 requested) and removed 37 (20 requested) atoms. Cycle 44: After refmac, R = 0.2033 (Rfree = 0.000) for 7416 atoms. Found 40 (40 requested) and removed 25 (20 requested) atoms. Cycle 45: After refmac, R = 0.2076 (Rfree = 0.000) for 7413 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 7633 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7651 seeds are put forward Round 1: 306 peptides, 65 chains. Longest chain 9 peptides. Score 0.249 Round 2: 374 peptides, 68 chains. Longest chain 11 peptides. Score 0.337 Round 3: 396 peptides, 65 chains. Longest chain 17 peptides. Score 0.389 Round 4: 375 peptides, 57 chains. Longest chain 18 peptides. Score 0.410 Round 5: 397 peptides, 67 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 318, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl5-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (318 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11385 reflections ( 99.89 % complete ) and 17647 restraints for refining 7438 atoms. 16398 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2119 (Rfree = 0.000) for 7438 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 7389 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2091 (Rfree = 0.000) for 7346 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 7306 atoms. TimeTaking 70.7