null Mon 24 Dec 00:45:45 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 1vqy-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqy-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-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/1vqy-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-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 ============================================================ Mon 24 Dec 00:45:50 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/1vqy-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqy-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.6016 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7424 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: 29.074 3.800 Wilson plot Bfac: 53.20 9994 reflections ( 98.35 % complete ) and 0 restraints for refining 8239 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.2896 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2850 (Rfree = 0.000) for 8239 atoms. Found 45 (45 requested) and removed 49 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 8382 seeds are put forward NCS extension: 0 residues added, 8382 seeds are put forward Round 1: 327 peptides, 68 chains. Longest chain 10 peptides. Score 0.275 Round 2: 432 peptides, 76 chains. Longest chain 23 peptides. Score 0.399 Round 3: 509 peptides, 78 chains. Longest chain 18 peptides. Score 0.503 Round 4: 516 peptides, 71 chains. Longest chain 19 peptides. Score 0.555 Round 5: 521 peptides, 66 chains. Longest chain 24 peptides. Score 0.590 Taking the results from Round 5 Chains 71, Residues 455, Estimated correctness of the model 0.0 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 14639 restraints for refining 6715 atoms. 12646 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 6715 atoms. Found 29 (36 requested) and removed 55 (18 requested) atoms. Cycle 2: After refmac, R = 0.2529 (Rfree = 0.000) for 6563 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 6490 atoms. Found 12 (36 requested) and removed 38 (18 requested) atoms. Cycle 4: After refmac, R = 0.1949 (Rfree = 0.000) for 6430 atoms. Found 22 (35 requested) and removed 31 (17 requested) atoms. Cycle 5: After refmac, R = 0.1870 (Rfree = 0.000) for 6397 atoms. Found 9 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 6592 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6604 seeds are put forward Round 1: 481 peptides, 82 chains. Longest chain 17 peptides. Score 0.436 Round 2: 522 peptides, 74 chains. Longest chain 20 peptides. Score 0.545 Round 3: 536 peptides, 73 chains. Longest chain 24 peptides. Score 0.569 Round 4: 508 peptides, 69 chains. Longest chain 21 peptides. Score 0.556 Round 5: 528 peptides, 71 chains. Longest chain 26 peptides. Score 0.570 Taking the results from Round 5 Chains 72, Residues 457, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15125 restraints for refining 6713 atoms. 13278 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2331 (Rfree = 0.000) for 6713 atoms. Found 36 (36 requested) and removed 57 (18 requested) atoms. Cycle 7: After refmac, R = 0.2188 (Rfree = 0.000) for 6626 atoms. Found 36 (36 requested) and removed 43 (18 requested) atoms. Cycle 8: After refmac, R = 0.1804 (Rfree = 0.000) for 6569 atoms. Found 15 (36 requested) and removed 35 (18 requested) atoms. Cycle 9: After refmac, R = 0.1719 (Rfree = 0.000) for 6524 atoms. Found 12 (36 requested) and removed 25 (18 requested) atoms. Cycle 10: After refmac, R = 0.1670 (Rfree = 0.000) for 6494 atoms. Found 9 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 6722 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6742 seeds are put forward Round 1: 440 peptides, 86 chains. Longest chain 10 peptides. Score 0.341 Round 2: 516 peptides, 78 chains. Longest chain 19 peptides. Score 0.513 Round 3: 532 peptides, 83 chains. Longest chain 23 peptides. Score 0.505 Round 4: 513 peptides, 75 chains. Longest chain 19 peptides. Score 0.527 Round 5: 534 peptides, 76 chains. Longest chain 20 peptides. Score 0.549 Taking the results from Round 5 Chains 78, Residues 458, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15048 restraints for refining 6714 atoms. 13212 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 6714 atoms. Found 36 (36 requested) and removed 54 (18 requested) atoms. Cycle 12: After refmac, R = 0.2274 (Rfree = 0.000) for 6629 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 6569 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 14: After refmac, R = 0.1756 (Rfree = 0.000) for 6526 atoms. Found 13 (36 requested) and removed 29 (18 requested) atoms. Cycle 15: After refmac, R = 0.1708 (Rfree = 0.000) for 6487 atoms. Found 10 (35 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 6644 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 6665 seeds are put forward Round 1: 393 peptides, 76 chains. Longest chain 10 peptides. Score 0.333 Round 2: 478 peptides, 78 chains. Longest chain 11 peptides. Score 0.457 Round 3: 504 peptides, 77 chains. Longest chain 18 peptides. Score 0.502 Round 4: 499 peptides, 72 chains. Longest chain 19 peptides. Score 0.526 Round 5: 492 peptides, 72 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 4 Chains 72, Residues 427, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15646 restraints for refining 6715 atoms. 14010 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2439 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 68 (18 requested) atoms. Cycle 17: After refmac, R = 0.2293 (Rfree = 0.000) for 6637 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 18: After refmac, R = 0.1833 (Rfree = 0.000) for 6601 atoms. Found 13 (36 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.1749 (Rfree = 0.000) for 6562 atoms. Found 7 (36 requested) and removed 23 (18 requested) atoms. Cycle 20: After refmac, R = 0.1711 (Rfree = 0.000) for 6534 atoms. Found 7 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 6749 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6771 seeds are put forward Round 1: 385 peptides, 72 chains. Longest chain 15 peptides. Score 0.349 Round 2: 447 peptides, 71 chains. Longest chain 22 peptides. Score 0.456 Round 3: 474 peptides, 77 chains. Longest chain 19 peptides. Score 0.458 Round 4: 492 peptides, 74 chains. Longest chain 29 peptides. Score 0.503 Round 5: 469 peptides, 75 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 4 Chains 78, Residues 418, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15308 restraints for refining 6715 atoms. 13583 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2457 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. Cycle 22: After refmac, R = 0.2337 (Rfree = 0.000) for 6652 atoms. Found 36 (36 requested) and removed 44 (18 requested) atoms. Cycle 23: After refmac, R = 0.2282 (Rfree = 0.000) for 6611 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 24: After refmac, R = 0.2258 (Rfree = 0.000) for 6575 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 25: After refmac, R = 0.1825 (Rfree = 0.000) for 6562 atoms. Found 14 (36 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 6709 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 6747 seeds are put forward Round 1: 352 peptides, 72 chains. Longest chain 10 peptides. Score 0.290 Round 2: 435 peptides, 72 chains. Longest chain 18 peptides. Score 0.431 Round 3: 443 peptides, 72 chains. Longest chain 14 peptides. Score 0.443 Round 4: 442 peptides, 67 chains. Longest chain 15 peptides. Score 0.475 Round 5: 444 peptides, 66 chains. Longest chain 22 peptides. Score 0.485 Taking the results from Round 5 Chains 68, Residues 378, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15595 restraints for refining 6715 atoms. 14092 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2331 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 27: After refmac, R = 0.2315 (Rfree = 0.000) for 6667 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. Cycle 28: After refmac, R = 0.2191 (Rfree = 0.000) for 6627 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 29: After refmac, R = 0.2102 (Rfree = 0.000) for 6613 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 30: After refmac, R = 0.2072 (Rfree = 0.000) for 6600 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 6760 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6777 seeds are put forward Round 1: 375 peptides, 80 chains. Longest chain 10 peptides. Score 0.271 Round 2: 425 peptides, 73 chains. Longest chain 19 peptides. Score 0.408 Round 3: 422 peptides, 74 chains. Longest chain 13 peptides. Score 0.396 Round 4: 405 peptides, 68 chains. Longest chain 14 peptides. Score 0.411 Round 5: 420 peptides, 72 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 4 Chains 68, Residues 337, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15755 restraints for refining 6707 atoms. 14475 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2200 (Rfree = 0.000) for 6707 atoms. Found 36 (36 requested) and removed 49 (18 requested) atoms. Cycle 32: After refmac, R = 0.2065 (Rfree = 0.000) for 6649 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 33: After refmac, R = 0.2047 (Rfree = 0.000) for 6625 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 34: After refmac, R = 0.1922 (Rfree = 0.000) for 6617 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 35: After refmac, R = 0.1558 (Rfree = 0.000) for 6611 atoms. Found 14 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 6790 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6809 seeds are put forward Round 1: 332 peptides, 73 chains. Longest chain 11 peptides. Score 0.245 Round 2: 398 peptides, 74 chains. Longest chain 13 peptides. Score 0.356 Round 3: 385 peptides, 67 chains. Longest chain 16 peptides. Score 0.385 Round 4: 399 peptides, 66 chains. Longest chain 23 peptides. Score 0.415 Round 5: 385 peptides, 65 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 4 Chains 67, Residues 333, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15584 restraints for refining 6696 atoms. 14278 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2309 (Rfree = 0.000) for 6696 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 37: After refmac, R = 0.2280 (Rfree = 0.000) for 6637 atoms. Found 36 (36 requested) and removed 43 (18 requested) atoms. Cycle 38: After refmac, R = 0.2153 (Rfree = 0.000) for 6609 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 39: After refmac, R = 0.2165 (Rfree = 0.000) for 6585 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 40: After refmac, R = 0.2104 (Rfree = 0.000) for 6574 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6743 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6755 seeds are put forward Round 1: 302 peptides, 67 chains. Longest chain 8 peptides. Score 0.235 Round 2: 354 peptides, 66 chains. Longest chain 17 peptides. Score 0.339 Round 3: 367 peptides, 68 chains. Longest chain 13 peptides. Score 0.347 Round 4: 356 peptides, 64 chains. Longest chain 13 peptides. Score 0.358 Round 5: 363 peptides, 65 chains. Longest chain 14 peptides. Score 0.362 Taking the results from Round 5 Chains 65, Residues 298, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15656 restraints for refining 6623 atoms. 14529 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2178 (Rfree = 0.000) for 6623 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. Cycle 42: After refmac, R = 0.2189 (Rfree = 0.000) for 6593 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. Cycle 43: After refmac, R = 0.2092 (Rfree = 0.000) for 6573 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. Cycle 44: After refmac, R = 0.2040 (Rfree = 0.000) for 6557 atoms. Found 36 (36 requested) and removed 24 (18 requested) atoms. Cycle 45: After refmac, R = 0.1655 (Rfree = 0.000) for 6552 atoms. Found 18 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 6695 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 6714 seeds are put forward Round 1: 285 peptides, 64 chains. Longest chain 9 peptides. Score 0.226 Round 2: 337 peptides, 63 chains. Longest chain 21 peptides. Score 0.332 Round 3: 338 peptides, 64 chains. Longest chain 11 peptides. Score 0.326 Round 4: 325 peptides, 60 chains. Longest chain 11 peptides. Score 0.333 Round 5: 332 peptides, 64 chains. Longest chain 12 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9994 reflections ( 98.35 % complete ) and 15401 restraints for refining 6509 atoms. 14401 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2174 (Rfree = 0.000) for 6509 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2154 (Rfree = 0.000) for 6464 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1769 (Rfree = 0.000) for 6437 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1692 (Rfree = 0.000) for 6409 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:52:03 GMT 2018 Job finished. TimeTaking 66.29 Used memory is bytes: 15081080