Mon 24 Dec 00:15:06 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 2pgc-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pgc-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 00:15:11 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/2pgc-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 742 and 0 Target number of residues in the AU: 742 Target solvent content: 0.6561 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.80 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: 98.043 3.600 Wilson plot Bfac: 82.18 14118 reflections ( 99.56 % complete ) and 0 restraints for refining 9206 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3347 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 9206 atoms. Found 59 (59 requested) and removed 43 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 9439 seeds are put forward NCS extension: 0 residues added, 9439 seeds are put forward Round 1: 432 peptides, 80 chains. Longest chain 15 peptides. Score 0.345 Round 2: 538 peptides, 78 chains. Longest chain 19 peptides. Score 0.499 Round 3: 569 peptides, 76 chains. Longest chain 19 peptides. Score 0.546 Round 4: 612 peptides, 71 chains. Longest chain 29 peptides. Score 0.616 Round 5: 608 peptides, 66 chains. Longest chain 23 peptides. Score 0.635 Taking the results from Round 5 Chains 71, Residues 542, Estimated correctness of the model 27.8 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16272 restraints for refining 7506 atoms. 13970 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2823 (Rfree = 0.000) for 7506 atoms. Found 48 (48 requested) and removed 50 (24 requested) atoms. Cycle 2: After refmac, R = 0.2629 (Rfree = 0.000) for 7394 atoms. Found 44 (48 requested) and removed 32 (24 requested) atoms. Cycle 3: After refmac, R = 0.2294 (Rfree = 0.000) for 7346 atoms. Found 19 (47 requested) and removed 27 (23 requested) atoms. Cycle 4: After refmac, R = 0.2283 (Rfree = 0.000) for 7311 atoms. Found 14 (47 requested) and removed 27 (23 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 7286 atoms. Found 3 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 7554 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 7571 seeds are put forward Round 1: 530 peptides, 82 chains. Longest chain 19 peptides. Score 0.467 Round 2: 589 peptides, 74 chains. Longest chain 26 peptides. Score 0.578 Round 3: 583 peptides, 67 chains. Longest chain 21 peptides. Score 0.605 Round 4: 595 peptides, 68 chains. Longest chain 27 peptides. Score 0.613 Round 5: 604 peptides, 68 chains. Longest chain 38 peptides. Score 0.622 Taking the results from Round 5 Chains 74, Residues 536, Estimated correctness of the model 23.0 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16385 restraints for refining 7505 atoms. 14088 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2594 (Rfree = 0.000) for 7505 atoms. Found 33 (48 requested) and removed 43 (24 requested) atoms. Cycle 7: After refmac, R = 0.2352 (Rfree = 0.000) for 7457 atoms. Found 20 (48 requested) and removed 36 (24 requested) atoms. Cycle 8: After refmac, R = 0.2226 (Rfree = 0.000) for 7412 atoms. Found 8 (47 requested) and removed 28 (23 requested) atoms. Cycle 9: After refmac, R = 0.2231 (Rfree = 0.000) for 7383 atoms. Found 11 (47 requested) and removed 25 (23 requested) atoms. Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 7365 atoms. Found 11 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 7634 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 7648 seeds are put forward Round 1: 507 peptides, 84 chains. Longest chain 14 peptides. Score 0.426 Round 2: 570 peptides, 74 chains. Longest chain 23 peptides. Score 0.557 Round 3: 568 peptides, 71 chains. Longest chain 18 peptides. Score 0.570 Round 4: 572 peptides, 73 chains. Longest chain 21 peptides. Score 0.564 Round 5: 565 peptides, 72 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 3 Chains 74, Residues 497, Estimated correctness of the model 2.6 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16904 restraints for refining 7505 atoms. 14861 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2638 (Rfree = 0.000) for 7505 atoms. Found 34 (48 requested) and removed 43 (24 requested) atoms. Cycle 12: After refmac, R = 0.2495 (Rfree = 0.000) for 7410 atoms. Found 48 (48 requested) and removed 40 (24 requested) atoms. Cycle 13: After refmac, R = 0.2339 (Rfree = 0.000) for 7355 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. Cycle 14: After refmac, R = 0.2308 (Rfree = 0.000) for 7329 atoms. Found 31 (47 requested) and removed 32 (23 requested) atoms. Cycle 15: After refmac, R = 0.2637 (Rfree = 0.000) for 7295 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 7606 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 7617 seeds are put forward Round 1: 446 peptides, 78 chains. Longest chain 13 peptides. Score 0.378 Round 2: 526 peptides, 76 chains. Longest chain 17 peptides. Score 0.495 Round 3: 554 peptides, 75 chains. Longest chain 22 peptides. Score 0.534 Round 4: 541 peptides, 71 chains. Longest chain 18 peptides. Score 0.540 Round 5: 566 peptides, 74 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 5 Chains 75, Residues 492, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17013 restraints for refining 7506 atoms. 15090 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3087 (Rfree = 0.000) for 7506 atoms. Found 48 (48 requested) and removed 86 (24 requested) atoms. Cycle 17: After refmac, R = 0.2805 (Rfree = 0.000) for 7356 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 18: After refmac, R = 0.2767 (Rfree = 0.000) for 7293 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 19: After refmac, R = 0.2643 (Rfree = 0.000) for 7248 atoms. Found 46 (46 requested) and removed 43 (23 requested) atoms. Cycle 20: After refmac, R = 0.2438 (Rfree = 0.000) for 7193 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 7434 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7447 seeds are put forward Round 1: 431 peptides, 84 chains. Longest chain 16 peptides. Score 0.319 Round 2: 506 peptides, 81 chains. Longest chain 15 peptides. Score 0.442 Round 3: 515 peptides, 83 chains. Longest chain 21 peptides. Score 0.442 Round 4: 535 peptides, 80 chains. Longest chain 20 peptides. Score 0.485 Round 5: 552 peptides, 78 chains. Longest chain 18 peptides. Score 0.516 Taking the results from Round 5 Chains 78, Residues 474, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17169 restraints for refining 7506 atoms. 15351 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2549 (Rfree = 0.000) for 7506 atoms. Found 39 (48 requested) and removed 41 (24 requested) atoms. Cycle 22: After refmac, R = 0.2384 (Rfree = 0.000) for 7424 atoms. Found 48 (48 requested) and removed 38 (24 requested) atoms. Cycle 23: After refmac, R = 0.2136 (Rfree = 0.000) for 7387 atoms. Found 42 (47 requested) and removed 33 (23 requested) atoms. Cycle 24: After refmac, R = 0.2031 (Rfree = 0.000) for 7376 atoms. Found 38 (47 requested) and removed 33 (23 requested) atoms. Cycle 25: After refmac, R = 0.1918 (Rfree = 0.000) for 7345 atoms. Found 31 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 7626 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7640 seeds are put forward Round 1: 412 peptides, 83 chains. Longest chain 10 peptides. Score 0.297 Round 2: 481 peptides, 79 chains. Longest chain 18 peptides. Score 0.420 Round 3: 486 peptides, 70 chains. Longest chain 18 peptides. Score 0.479 Round 4: 500 peptides, 73 chains. Longest chain 21 peptides. Score 0.480 Round 5: 491 peptides, 70 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 5 Chains 70, Residues 421, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17351 restraints for refining 7505 atoms. 15737 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 7505 atoms. Found 46 (48 requested) and removed 36 (24 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 7471 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 28: After refmac, R = 0.1725 (Rfree = 0.000) for 7456 atoms. Found 7 (48 requested) and removed 27 (24 requested) atoms. Cycle 29: After refmac, R = 0.1627 (Rfree = 0.000) for 7420 atoms. Found 7 (47 requested) and removed 28 (23 requested) atoms. Cycle 30: After refmac, R = 0.1614 (Rfree = 0.000) for 7392 atoms. Found 11 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 7647 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7665 seeds are put forward Round 1: 409 peptides, 81 chains. Longest chain 9 peptides. Score 0.305 Round 2: 445 peptides, 73 chains. Longest chain 15 peptides. Score 0.407 Round 3: 458 peptides, 67 chains. Longest chain 19 peptides. Score 0.460 Round 4: 478 peptides, 72 chains. Longest chain 22 peptides. Score 0.457 Round 5: 462 peptides, 69 chains. Longest chain 20 peptides. Score 0.454 Taking the results from Round 3 Chains 67, Residues 391, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17510 restraints for refining 7506 atoms. 15998 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1996 (Rfree = 0.000) for 7506 atoms. Found 31 (48 requested) and removed 31 (24 requested) atoms. Cycle 32: After refmac, R = 0.1963 (Rfree = 0.000) for 7469 atoms. Found 36 (48 requested) and removed 29 (24 requested) atoms. Cycle 33: After refmac, R = 0.1897 (Rfree = 0.000) for 7455 atoms. Found 42 (47 requested) and removed 27 (23 requested) atoms. Cycle 34: After refmac, R = 0.1906 (Rfree = 0.000) for 7457 atoms. Found 41 (47 requested) and removed 28 (23 requested) atoms. Cycle 35: After refmac, R = 0.1594 (Rfree = 0.000) for 7457 atoms. Found 15 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 7699 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7718 seeds are put forward Round 1: 388 peptides, 82 chains. Longest chain 8 peptides. Score 0.266 Round 2: 453 peptides, 77 chains. Longest chain 13 peptides. Score 0.394 Round 3: 469 peptides, 77 chains. Longest chain 16 peptides. Score 0.416 Round 4: 476 peptides, 76 chains. Longest chain 13 peptides. Score 0.431 Round 5: 480 peptides, 67 chains. Longest chain 23 peptides. Score 0.488 Taking the results from Round 5 Chains 67, Residues 413, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17245 restraints for refining 7505 atoms. 15610 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2026 (Rfree = 0.000) for 7505 atoms. Found 31 (48 requested) and removed 33 (24 requested) atoms. Cycle 37: After refmac, R = 0.1893 (Rfree = 0.000) for 7475 atoms. Found 24 (48 requested) and removed 25 (24 requested) atoms. Cycle 38: After refmac, R = 0.1873 (Rfree = 0.000) for 7462 atoms. Found 32 (47 requested) and removed 26 (23 requested) atoms. Cycle 39: After refmac, R = 0.1793 (Rfree = 0.000) for 7457 atoms. Found 30 (47 requested) and removed 24 (23 requested) atoms. Cycle 40: After refmac, R = 0.1861 (Rfree = 0.000) for 7443 atoms. Found 32 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 7686 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 7711 seeds are put forward Round 1: 347 peptides, 72 chains. Longest chain 12 peptides. Score 0.267 Round 2: 417 peptides, 70 chains. Longest chain 14 peptides. Score 0.386 Round 3: 401 peptides, 71 chains. Longest chain 13 peptides. Score 0.357 Round 4: 403 peptides, 64 chains. Longest chain 18 peptides. Score 0.404 Round 5: 394 peptides, 63 chains. Longest chain 15 peptides. Score 0.397 Taking the results from Round 4 Chains 66, Residues 339, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17676 restraints for refining 7506 atoms. 16357 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1967 (Rfree = 0.000) for 7506 atoms. Found 33 (48 requested) and removed 26 (24 requested) atoms. Cycle 42: After refmac, R = 0.1840 (Rfree = 0.000) for 7498 atoms. Found 11 (48 requested) and removed 26 (24 requested) atoms. Cycle 43: After refmac, R = 0.1902 (Rfree = 0.000) for 7474 atoms. Found 28 (48 requested) and removed 26 (24 requested) atoms. Cycle 44: After refmac, R = 0.1959 (Rfree = 0.000) for 7466 atoms. Found 34 (47 requested) and removed 26 (23 requested) atoms. Cycle 45: After refmac, R = 0.1809 (Rfree = 0.000) for 7469 atoms. Found 16 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 7679 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7697 seeds are put forward Round 1: 318 peptides, 65 chains. Longest chain 11 peptides. Score 0.268 Round 2: 376 peptides, 67 chains. Longest chain 12 peptides. Score 0.345 Round 3: 405 peptides, 66 chains. Longest chain 13 peptides. Score 0.394 Round 4: 380 peptides, 66 chains. Longest chain 16 peptides. Score 0.358 Round 5: 392 peptides, 62 chains. Longest chain 16 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 330, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 62 chains (330 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14118 reflections ( 99.56 % complete ) and 17724 restraints for refining 7503 atoms. 16453 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1971 (Rfree = 0.000) for 7503 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 7453 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1842 (Rfree = 0.000) for 7419 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1798 (Rfree = 0.000) for 7388 atoms. TimeTaking 90.72