Mon 24 Dec 07:27:21 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqr-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqr-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-noncs ############### 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 07:27:25 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/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqr-3.4-parrot-noncs/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 923 and 0 Target number of residues in the AU: 923 Target solvent content: 0.6017 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.4-parrot-noncs.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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 3.400 Wilson plot Bfac: 53.18 15170 reflections ( 88.81 % complete ) and 0 restraints for refining 10610 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3595 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3102 (Rfree = 0.000) for 10610 atoms. Found 64 (80 requested) and removed 137 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.12 Search for helices and strands: 0 residues in 0 chains, 10667 seeds are put forward NCS extension: 0 residues added, 10667 seeds are put forward Round 1: 282 peptides, 60 chains. Longest chain 9 peptides. Score 0.239 Round 2: 394 peptides, 84 chains. Longest chain 8 peptides. Score 0.257 Round 3: 407 peptides, 77 chains. Longest chain 12 peptides. Score 0.319 Round 4: 415 peptides, 78 chains. Longest chain 12 peptides. Score 0.325 Round 5: 431 peptides, 75 chains. Longest chain 12 peptides. Score 0.365 Taking the results from Round 5 Chains 75, Residues 356, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20723 restraints for refining 8640 atoms. 19342 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2519 (Rfree = 0.000) for 8640 atoms. Found 37 (65 requested) and removed 52 (32 requested) atoms. Cycle 2: After refmac, R = 0.2449 (Rfree = 0.000) for 8549 atoms. Found 38 (65 requested) and removed 41 (32 requested) atoms. Cycle 3: After refmac, R = 0.2340 (Rfree = 0.000) for 8509 atoms. Found 25 (64 requested) and removed 43 (32 requested) atoms. Cycle 4: After refmac, R = 0.2280 (Rfree = 0.000) for 8456 atoms. Found 27 (64 requested) and removed 40 (32 requested) atoms. Cycle 5: After refmac, R = 0.2189 (Rfree = 0.000) for 8410 atoms. Found 27 (63 requested) and removed 44 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 3.13 Search for helices and strands: 0 residues in 0 chains, 8604 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8621 seeds are put forward Round 1: 398 peptides, 86 chains. Longest chain 10 peptides. Score 0.251 Round 2: 462 peptides, 89 chains. Longest chain 10 peptides. Score 0.325 Round 3: 459 peptides, 81 chains. Longest chain 15 peptides. Score 0.367 Round 4: 470 peptides, 78 chains. Longest chain 18 peptides. Score 0.399 Round 5: 481 peptides, 81 chains. Longest chain 27 peptides. Score 0.396 Taking the results from Round 4 Chains 78, Residues 392, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 19987 restraints for refining 8380 atoms. 18441 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2285 (Rfree = 0.000) for 8380 atoms. Found 55 (63 requested) and removed 59 (31 requested) atoms. Cycle 7: After refmac, R = 0.2152 (Rfree = 0.000) for 8340 atoms. Found 27 (63 requested) and removed 37 (31 requested) atoms. Cycle 8: After refmac, R = 0.2098 (Rfree = 0.000) for 8300 atoms. Found 24 (62 requested) and removed 40 (31 requested) atoms. Cycle 9: After refmac, R = 0.2056 (Rfree = 0.000) for 8266 atoms. Found 31 (62 requested) and removed 44 (31 requested) atoms. Cycle 10: After refmac, R = 0.1951 (Rfree = 0.000) for 8237 atoms. Found 17 (62 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 8431 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8452 seeds are put forward Round 1: 419 peptides, 83 chains. Longest chain 14 peptides. Score 0.300 Round 2: 480 peptides, 85 chains. Longest chain 11 peptides. Score 0.372 Round 3: 486 peptides, 81 chains. Longest chain 14 peptides. Score 0.403 Round 4: 471 peptides, 80 chains. Longest chain 13 peptides. Score 0.389 Round 5: 473 peptides, 78 chains. Longest chain 14 peptides. Score 0.403 Taking the results from Round 5 Chains 78, Residues 395, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20125 restraints for refining 8587 atoms. 18558 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2134 (Rfree = 0.000) for 8587 atoms. Found 48 (64 requested) and removed 55 (32 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1969 (Rfree = 0.000) for 8555 atoms. Found 20 (64 requested) and removed 43 (32 requested) atoms. Cycle 13: After refmac, R = 0.1942 (Rfree = 0.000) for 8520 atoms. Found 14 (64 requested) and removed 36 (32 requested) atoms. Cycle 14: After refmac, R = 0.1960 (Rfree = 0.000) for 8488 atoms. Found 15 (64 requested) and removed 35 (32 requested) atoms. Cycle 15: After refmac, R = 0.1992 (Rfree = 0.000) for 8459 atoms. Found 24 (63 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 8634 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 8653 seeds are put forward Round 1: 418 peptides, 83 chains. Longest chain 10 peptides. Score 0.299 Round 2: 480 peptides, 83 chains. Longest chain 16 peptides. Score 0.384 Round 3: 468 peptides, 79 chains. Longest chain 12 peptides. Score 0.391 Round 4: 473 peptides, 83 chains. Longest chain 13 peptides. Score 0.374 Round 5: 494 peptides, 86 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 3 Chains 79, Residues 389, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15170 reflections ( 88.81 % complete ) and 20488 restraints for refining 8634 atoms. 18989 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2084 (Rfree = 0.000) for 8634 atoms. Found 41 (65 requested) and removed 50 (32 requested) atoms. Cycle 17: After refmac, R = 0.2043 (Rfree = 0.000) for 8611 atoms. Found 34 (65 requested) and removed 43 (32 requested) atoms. Cycle 18: After refmac, R = 0.1995 (Rfree = 0.000) for 8592 atoms. Found 30 (64 requested) and removed 41 (32 requested) atoms. Cycle 19: After refmac, R = 0.1907 (Rfree = 0.000) for 8570 atoms. Found 18 (64 requested) and removed 38 (32 requested) atoms. Cycle 20: After refmac, R = 0.1879 (Rfree = 0.000) for 8543 atoms. Found 15 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 8732 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8750 seeds are put forward Round 1: 420 peptides, 92 chains. Longest chain 9 peptides. Score 0.247 Round 2: 465 peptides, 86 chains. Longest chain 14 peptides. Score 0.346 Round 3: 469 peptides, 83 chains. Longest chain 16 peptides. Score 0.369 Round 4: 478 peptides, 79 chains. Longest chain 17 peptides. Score 0.404 Round 5: 492 peptides, 85 chains. Longest chain 18 peptides. Score 0.388 Taking the results from Round 4 Chains 79, Residues 399, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20395 restraints for refining 8641 atoms. 18851 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2156 (Rfree = 0.000) for 8641 atoms. Found 37 (65 requested) and removed 47 (32 requested) atoms. Cycle 22: After refmac, R = 0.2022 (Rfree = 0.000) for 8608 atoms. Found 43 (65 requested) and removed 42 (32 requested) atoms. Cycle 23: After refmac, R = 0.1951 (Rfree = 0.000) for 8592 atoms. Found 22 (65 requested) and removed 36 (32 requested) atoms. Cycle 24: After refmac, R = 0.1949 (Rfree = 0.000) for 8568 atoms. Found 33 (64 requested) and removed 36 (32 requested) atoms. Cycle 25: After refmac, R = 0.1893 (Rfree = 0.000) for 8557 atoms. Found 16 (64 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 8759 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 8786 seeds are put forward Round 1: 393 peptides, 83 chains. Longest chain 13 peptides. Score 0.262 Round 2: 458 peptides, 83 chains. Longest chain 16 peptides. Score 0.354 Round 3: 471 peptides, 82 chains. Longest chain 17 peptides. Score 0.378 Round 4: 474 peptides, 79 chains. Longest chain 21 peptides. Score 0.399 Round 5: 455 peptides, 80 chains. Longest chain 16 peptides. Score 0.368 Taking the results from Round 4 Chains 80, Residues 395, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20366 restraints for refining 8640 atoms. 18825 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1999 (Rfree = 0.000) for 8640 atoms. Found 40 (65 requested) and removed 37 (32 requested) atoms. Cycle 27: After refmac, R = 0.1904 (Rfree = 0.000) for 8623 atoms. Found 21 (65 requested) and removed 33 (32 requested) atoms. Cycle 28: After refmac, R = 0.1944 (Rfree = 0.000) for 8602 atoms. Found 22 (65 requested) and removed 37 (32 requested) atoms. Cycle 29: After refmac, R = 0.1900 (Rfree = 0.000) for 8576 atoms. Found 16 (64 requested) and removed 36 (32 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 8544 atoms. Found 13 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.14 Search for helices and strands: 0 residues in 0 chains, 8699 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 8732 seeds are put forward Round 1: 404 peptides, 86 chains. Longest chain 12 peptides. Score 0.260 Round 2: 472 peptides, 90 chains. Longest chain 10 peptides. Score 0.333 Round 3: 482 peptides, 87 chains. Longest chain 11 peptides. Score 0.364 Round 4: 465 peptides, 85 chains. Longest chain 13 peptides. Score 0.352 Round 5: 478 peptides, 86 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Chains 87, Residues 392, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20239 restraints for refining 8641 atoms. 18653 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2003 (Rfree = 0.000) for 8641 atoms. Found 52 (65 requested) and removed 40 (32 requested) atoms. Cycle 32: After refmac, R = 0.1864 (Rfree = 0.000) for 8635 atoms. Found 13 (65 requested) and removed 33 (32 requested) atoms. Cycle 33: After refmac, R = 0.1846 (Rfree = 0.000) for 8607 atoms. Found 9 (65 requested) and removed 32 (32 requested) atoms. Cycle 34: After refmac, R = 0.1926 (Rfree = 0.000) for 8574 atoms. Found 33 (64 requested) and removed 34 (32 requested) atoms. Cycle 35: After refmac, R = 0.1892 (Rfree = 0.000) for 8566 atoms. Found 26 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 8736 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8750 seeds are put forward Round 1: 407 peptides, 87 chains. Longest chain 8 peptides. Score 0.258 Round 2: 439 peptides, 80 chains. Longest chain 13 peptides. Score 0.346 Round 3: 426 peptides, 79 chains. Longest chain 11 peptides. Score 0.334 Round 4: 425 peptides, 74 chains. Longest chain 16 peptides. Score 0.362 Round 5: 439 peptides, 78 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 4 Chains 74, Residues 351, Estimated correctness of the model 0.0 % 6 chains (21 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20418 restraints for refining 8641 atoms. 19031 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2047 (Rfree = 0.000) for 8641 atoms. Found 35 (65 requested) and removed 38 (32 requested) atoms. Cycle 37: After refmac, R = 0.1977 (Rfree = 0.000) for 8623 atoms. Found 36 (65 requested) and removed 35 (32 requested) atoms. Cycle 38: After refmac, R = 0.1928 (Rfree = 0.000) for 8612 atoms. Found 28 (65 requested) and removed 40 (32 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1866 (Rfree = 0.000) for 8595 atoms. Found 16 (64 requested) and removed 33 (32 requested) atoms. Cycle 40: After refmac, R = 0.1863 (Rfree = 0.000) for 8572 atoms. Found 20 (64 requested) and removed 32 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 8749 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8766 seeds are put forward Round 1: 362 peptides, 78 chains. Longest chain 8 peptides. Score 0.247 Round 2: 418 peptides, 78 chains. Longest chain 12 peptides. Score 0.329 Round 3: 405 peptides, 72 chains. Longest chain 12 peptides. Score 0.347 Round 4: 408 peptides, 74 chains. Longest chain 14 peptides. Score 0.339 Round 5: 394 peptides, 68 chains. Longest chain 11 peptides. Score 0.356 Taking the results from Round 5 Chains 68, Residues 326, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 15170 reflections ( 88.81 % complete ) and 20656 restraints for refining 8640 atoms. 19404 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 8640 atoms. Found 41 (65 requested) and removed 34 (32 requested) atoms. Cycle 42: After refmac, R = 0.1924 (Rfree = 0.000) for 8636 atoms. Found 29 (65 requested) and removed 33 (32 requested) atoms. Cycle 43: After refmac, R = 0.1954 (Rfree = 0.000) for 8626 atoms. Found 29 (65 requested) and removed 35 (32 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 8617 atoms. Found 22 (65 requested) and removed 32 (32 requested) atoms. Cycle 45: After refmac, R = 0.1855 (Rfree = 0.000) for 8602 atoms. Found 22 (64 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.13 Search for helices and strands: 0 residues in 0 chains, 8746 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 8758 seeds are put forward Round 1: 361 peptides, 78 chains. Longest chain 10 peptides. Score 0.245 Round 2: 388 peptides, 72 chains. Longest chain 10 peptides. Score 0.323 Round 3: 419 peptides, 70 chains. Longest chain 12 peptides. Score 0.378 Round 4: 428 peptides, 75 chains. Longest chain 11 peptides. Score 0.361 Round 5: 417 peptides, 73 chains. Longest chain 14 peptides. Score 0.357 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 349, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (349 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15170 reflections ( 88.81 % complete ) and 20371 restraints for refining 8639 atoms. 19022 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1872 (Rfree = 0.000) for 8639 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.1888 (Rfree = 0.000) for 8594 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1863 (Rfree = 0.000) for 8552 atoms. Found 0 (64 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1837 (Rfree = 0.000) for 8516 atoms. TimeTaking 87.13