null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2okc-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.4-parrot-hancs ############### 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 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.4-parrot-hancs/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 642 and 0 Target number of residues in the AU: 642 Target solvent content: 0.6476 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-3.4-parrot-hancs.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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 7120 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: 28.546 3.400 Wilson plot Bfac: 76.60 12678 reflections ( 89.55 % complete ) and 0 restraints for refining 7881 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3236 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2906 (Rfree = 0.000) for 7881 atoms. Found 59 (59 requested) and removed 65 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 8019 seeds are put forward NCS extension: 0 residues added, 8019 seeds are put forward Round 1: 340 peptides, 67 chains. Longest chain 9 peptides. Score 0.306 Round 2: 417 peptides, 64 chains. Longest chain 18 peptides. Score 0.456 Round 3: 467 peptides, 70 chains. Longest chain 24 peptides. Score 0.491 Round 4: 468 peptides, 65 chains. Longest chain 27 peptides. Score 0.524 Round 5: 488 peptides, 65 chains. Longest chain 27 peptides. Score 0.551 Taking the results from Round 5 Chains 69, Residues 423, Estimated correctness of the model 11.9 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14409 restraints for refining 6473 atoms. 12644 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2558 (Rfree = 0.000) for 6473 atoms. Found 33 (48 requested) and removed 44 (24 requested) atoms. Cycle 2: After refmac, R = 0.2441 (Rfree = 0.000) for 6385 atoms. Found 31 (48 requested) and removed 42 (24 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 6341 atoms. Found 25 (48 requested) and removed 41 (24 requested) atoms. Cycle 4: After refmac, R = 0.2163 (Rfree = 0.000) for 6309 atoms. Found 11 (47 requested) and removed 34 (23 requested) atoms. Cycle 5: After refmac, R = 0.2182 (Rfree = 0.000) for 6273 atoms. Found 19 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 6479 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6497 seeds are put forward Round 1: 397 peptides, 70 chains. Longest chain 12 peptides. Score 0.382 Round 2: 455 peptides, 66 chains. Longest chain 17 peptides. Score 0.499 Round 3: 460 peptides, 64 chains. Longest chain 20 peptides. Score 0.519 Round 4: 449 peptides, 61 chains. Longest chain 22 peptides. Score 0.522 Round 5: 468 peptides, 58 chains. Longest chain 20 peptides. Score 0.566 Taking the results from Round 5 Chains 59, Residues 410, Estimated correctness of the model 17.2 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14274 restraints for refining 6474 atoms. 12501 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2381 (Rfree = 0.000) for 6474 atoms. Found 31 (48 requested) and removed 47 (24 requested) atoms. Cycle 7: After refmac, R = 0.2261 (Rfree = 0.000) for 6429 atoms. Found 41 (48 requested) and removed 38 (24 requested) atoms. Cycle 8: After refmac, R = 0.2186 (Rfree = 0.000) for 6413 atoms. Found 26 (48 requested) and removed 40 (24 requested) atoms. Cycle 9: After refmac, R = 0.1944 (Rfree = 0.000) for 6377 atoms. Found 15 (48 requested) and removed 28 (24 requested) atoms. Cycle 10: After refmac, R = 0.2019 (Rfree = 0.000) for 6345 atoms. Found 21 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 6570 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6592 seeds are put forward Round 1: 395 peptides, 72 chains. Longest chain 16 peptides. Score 0.365 Round 2: 448 peptides, 69 chains. Longest chain 17 peptides. Score 0.470 Round 3: 449 peptides, 67 chains. Longest chain 18 peptides. Score 0.484 Round 4: 455 peptides, 67 chains. Longest chain 15 peptides. Score 0.493 Round 5: 441 peptides, 62 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 5 Chains 64, Residues 379, Estimated correctness of the model 0.0 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14537 restraints for refining 6474 atoms. 12964 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2331 (Rfree = 0.000) for 6474 atoms. Found 44 (48 requested) and removed 55 (24 requested) atoms. Cycle 12: After refmac, R = 0.2198 (Rfree = 0.000) for 6434 atoms. Found 35 (48 requested) and removed 39 (24 requested) atoms. Cycle 13: After refmac, R = 0.2088 (Rfree = 0.000) for 6407 atoms. Found 24 (48 requested) and removed 35 (24 requested) atoms. Cycle 14: After refmac, R = 0.2036 (Rfree = 0.000) for 6382 atoms. Found 36 (48 requested) and removed 29 (24 requested) atoms. Cycle 15: After refmac, R = 0.2027 (Rfree = 0.000) for 6376 atoms. Found 31 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 6584 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6601 seeds are put forward Round 1: 395 peptides, 74 chains. Longest chain 13 peptides. Score 0.350 Round 2: 435 peptides, 67 chains. Longest chain 17 peptides. Score 0.463 Round 3: 431 peptides, 64 chains. Longest chain 16 peptides. Score 0.477 Round 4: 446 peptides, 66 chains. Longest chain 17 peptides. Score 0.486 Round 5: 439 peptides, 64 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 5 Chains 64, Residues 375, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14723 restraints for refining 6474 atoms. 13272 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2237 (Rfree = 0.000) for 6474 atoms. Found 46 (48 requested) and removed 36 (24 requested) atoms. Cycle 17: After refmac, R = 0.2120 (Rfree = 0.000) for 6463 atoms. Found 32 (48 requested) and removed 32 (24 requested) atoms. Cycle 18: After refmac, R = 0.2093 (Rfree = 0.000) for 6444 atoms. Found 36 (48 requested) and removed 31 (24 requested) atoms. Cycle 19: After refmac, R = 0.2006 (Rfree = 0.000) for 6429 atoms. Found 32 (48 requested) and removed 30 (24 requested) atoms. Cycle 20: After refmac, R = 0.1949 (Rfree = 0.000) for 6417 atoms. Found 25 (48 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 6595 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6618 seeds are put forward Round 1: 359 peptides, 70 chains. Longest chain 12 peptides. Score 0.317 Round 2: 416 peptides, 69 chains. Longest chain 14 peptides. Score 0.420 Round 3: 417 peptides, 66 chains. Longest chain 13 peptides. Score 0.442 Round 4: 433 peptides, 65 chains. Longest chain 14 peptides. Score 0.474 Round 5: 432 peptides, 64 chains. Longest chain 18 peptides. Score 0.479 Taking the results from Round 5 Chains 67, Residues 368, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14562 restraints for refining 6474 atoms. 13059 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2227 (Rfree = 0.000) for 6474 atoms. Found 33 (48 requested) and removed 38 (24 requested) atoms. Cycle 22: After refmac, R = 0.2132 (Rfree = 0.000) for 6445 atoms. Found 23 (48 requested) and removed 30 (24 requested) atoms. Cycle 23: After refmac, R = 0.2127 (Rfree = 0.000) for 6424 atoms. Found 39 (48 requested) and removed 34 (24 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 6414 atoms. Found 30 (48 requested) and removed 30 (24 requested) atoms. Cycle 25: After refmac, R = 0.2036 (Rfree = 0.000) for 6406 atoms. Found 34 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 6605 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6623 seeds are put forward Round 1: 388 peptides, 74 chains. Longest chain 16 peptides. Score 0.338 Round 2: 432 peptides, 73 chains. Longest chain 13 peptides. Score 0.418 Round 3: 407 peptides, 69 chains. Longest chain 12 peptides. Score 0.406 Round 4: 432 peptides, 68 chains. Longest chain 17 peptides. Score 0.452 Round 5: 417 peptides, 69 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 69, Residues 364, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14497 restraints for refining 6472 atoms. 13028 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2121 (Rfree = 0.000) for 6472 atoms. Found 44 (48 requested) and removed 40 (24 requested) atoms. Cycle 27: After refmac, R = 0.2038 (Rfree = 0.000) for 6456 atoms. Found 37 (48 requested) and removed 32 (24 requested) atoms. Cycle 28: After refmac, R = 0.2008 (Rfree = 0.000) for 6436 atoms. Found 32 (48 requested) and removed 34 (24 requested) atoms. Cycle 29: After refmac, R = 0.1943 (Rfree = 0.000) for 6423 atoms. Found 25 (48 requested) and removed 28 (24 requested) atoms. Cycle 30: After refmac, R = 0.1924 (Rfree = 0.000) for 6408 atoms. Found 32 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 6579 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6593 seeds are put forward Round 1: 335 peptides, 66 chains. Longest chain 11 peptides. Score 0.304 Round 2: 377 peptides, 62 chains. Longest chain 16 peptides. Score 0.407 Round 3: 385 peptides, 64 chains. Longest chain 22 peptides. Score 0.405 Round 4: 379 peptides, 56 chains. Longest chain 21 peptides. Score 0.452 Round 5: 361 peptides, 58 chains. Longest chain 21 peptides. Score 0.409 Taking the results from Round 4 Chains 57, Residues 323, Estimated correctness of the model 0.0 % 7 chains (45 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14411 restraints for refining 6473 atoms. 13046 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2234 (Rfree = 0.000) for 6473 atoms. Found 45 (48 requested) and removed 31 (24 requested) atoms. Cycle 32: After refmac, R = 0.2161 (Rfree = 0.000) for 6463 atoms. Found 47 (48 requested) and removed 27 (24 requested) atoms. Cycle 33: After refmac, R = 0.2157 (Rfree = 0.000) for 6465 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 34: After refmac, R = 0.2042 (Rfree = 0.000) for 6463 atoms. Found 31 (48 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.2007 (Rfree = 0.000) for 6452 atoms. Found 36 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 6639 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 6677 seeds are put forward Round 1: 306 peptides, 64 chains. Longest chain 11 peptides. Score 0.266 Round 2: 352 peptides, 67 chains. Longest chain 15 peptides. Score 0.327 Round 3: 352 peptides, 62 chains. Longest chain 16 peptides. Score 0.365 Round 4: 360 peptides, 59 chains. Longest chain 18 peptides. Score 0.400 Round 5: 333 peptides, 54 chains. Longest chain 18 peptides. Score 0.392 Taking the results from Round 4 Chains 60, Residues 301, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14725 restraints for refining 6472 atoms. 13492 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2129 (Rfree = 0.000) for 6472 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 37: After refmac, R = 0.2028 (Rfree = 0.000) for 6464 atoms. Found 33 (49 requested) and removed 29 (24 requested) atoms. Cycle 38: After refmac, R = 0.1987 (Rfree = 0.000) for 6454 atoms. Found 43 (48 requested) and removed 34 (24 requested) atoms. Cycle 39: After refmac, R = 0.1938 (Rfree = 0.000) for 6454 atoms. Found 42 (48 requested) and removed 27 (24 requested) atoms. Cycle 40: After refmac, R = 0.1933 (Rfree = 0.000) for 6466 atoms. Found 39 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 6613 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 6639 seeds are put forward Round 1: 302 peptides, 64 chains. Longest chain 11 peptides. Score 0.259 Round 2: 328 peptides, 65 chains. Longest chain 12 peptides. Score 0.299 Round 3: 349 peptides, 63 chains. Longest chain 10 peptides. Score 0.352 Round 4: 349 peptides, 61 chains. Longest chain 13 peptides. Score 0.367 Round 5: 343 peptides, 59 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 5 Chains 60, Residues 284, Estimated correctness of the model 0.0 % 8 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 15124 restraints for refining 6474 atoms. 13979 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2233 (Rfree = 0.000) for 6474 atoms. Found 39 (48 requested) and removed 62 (24 requested) atoms. Cycle 42: After refmac, R = 0.2087 (Rfree = 0.000) for 6438 atoms. Found 47 (48 requested) and removed 28 (24 requested) atoms. Cycle 43: After refmac, R = 0.2011 (Rfree = 0.000) for 6443 atoms. Found 45 (48 requested) and removed 32 (24 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 6447 atoms. Found 42 (48 requested) and removed 33 (24 requested) atoms. Cycle 45: After refmac, R = 0.1679 (Rfree = 0.000) for 6448 atoms. Found 14 (48 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 6568 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6582 seeds are put forward Round 1: 269 peptides, 55 chains. Longest chain 11 peptides. Score 0.268 Round 2: 326 peptides, 58 chains. Longest chain 15 peptides. Score 0.350 Round 3: 340 peptides, 60 chains. Longest chain 14 peptides. Score 0.359 Round 4: 313 peptides, 54 chains. Longest chain 13 peptides. Score 0.357 Round 5: 322 peptides, 54 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 268, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 54 chains (268 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12678 reflections ( 89.55 % complete ) and 15259 restraints for refining 6472 atoms. 14210 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2106 (Rfree = 0.000) for 6472 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2153 (Rfree = 0.000) for 6442 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1848 (Rfree = 0.000) for 6413 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.2084 (Rfree = 0.000) for 6382 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:46:27 GMT 2018 Job finished. TimeTaking 83.37 Used memory is bytes: 4393304