null Mon 24 Dec 07:27:53 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 2okc-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-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/2okc-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-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 07:27:57 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/2okc-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-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 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-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: 19 Cell parameters: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.4-parrot-noncs.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 7887 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2843 (Rfree = 0.000) for 7887 atoms. Found 59 (59 requested) and removed 49 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 8042 seeds are put forward NCS extension: 0 residues added, 8042 seeds are put forward Round 1: 355 peptides, 72 chains. Longest chain 11 peptides. Score 0.295 Round 2: 431 peptides, 72 chains. Longest chain 15 peptides. Score 0.423 Round 3: 480 peptides, 75 chains. Longest chain 17 peptides. Score 0.478 Round 4: 470 peptides, 67 chains. Longest chain 20 peptides. Score 0.514 Round 5: 497 peptides, 73 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 5 Chains 73, Residues 424, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14840 restraints for refining 6472 atoms. 13187 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2515 (Rfree = 0.000) for 6472 atoms. Found 48 (48 requested) and removed 46 (24 requested) atoms. Cycle 2: After refmac, R = 0.2451 (Rfree = 0.000) for 6399 atoms. Found 30 (48 requested) and removed 43 (24 requested) atoms. Cycle 3: After refmac, R = 0.2153 (Rfree = 0.000) for 6346 atoms. Found 22 (48 requested) and removed 32 (24 requested) atoms. Cycle 4: After refmac, R = 0.2049 (Rfree = 0.000) for 6315 atoms. Found 20 (47 requested) and removed 25 (23 requested) atoms. Cycle 5: After refmac, R = 0.1980 (Rfree = 0.000) for 6292 atoms. Found 2 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 6475 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6497 seeds are put forward Round 1: 447 peptides, 75 chains. Longest chain 16 peptides. Score 0.428 Round 2: 498 peptides, 76 chains. Longest chain 16 peptides. Score 0.498 Round 3: 508 peptides, 69 chains. Longest chain 21 peptides. Score 0.554 Round 4: 512 peptides, 70 chains. Longest chain 21 peptides. Score 0.553 Round 5: 516 peptides, 67 chains. Longest chain 21 peptides. Score 0.576 Taking the results from Round 5 Chains 71, Residues 449, Estimated correctness of the model 20.7 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14128 restraints for refining 6472 atoms. 12269 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2344 (Rfree = 0.000) for 6472 atoms. Found 29 (48 requested) and removed 46 (24 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 6407 atoms. Found 23 (48 requested) and removed 32 (24 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 6371 atoms. Found 15 (48 requested) and removed 34 (24 requested) atoms. Cycle 9: After refmac, R = 0.2155 (Rfree = 0.000) for 6334 atoms. Found 21 (47 requested) and removed 31 (23 requested) atoms. Cycle 10: After refmac, R = 0.1960 (Rfree = 0.000) for 6308 atoms. Found 8 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 6506 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6520 seeds are put forward Round 1: 439 peptides, 75 chains. Longest chain 13 peptides. Score 0.416 Round 2: 486 peptides, 75 chains. Longest chain 15 peptides. Score 0.487 Round 3: 470 peptides, 71 chains. Longest chain 21 peptides. Score 0.489 Round 4: 501 peptides, 78 chains. Longest chain 15 peptides. Score 0.490 Round 5: 474 peptides, 68 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 5 Chains 68, Residues 406, Estimated correctness of the model 0.0 % 8 chains (48 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14399 restraints for refining 6472 atoms. 12692 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2319 (Rfree = 0.000) for 6472 atoms. Found 38 (48 requested) and removed 45 (24 requested) atoms. Cycle 12: After refmac, R = 0.2216 (Rfree = 0.000) for 6427 atoms. Found 24 (48 requested) and removed 34 (24 requested) atoms. Cycle 13: After refmac, R = 0.2113 (Rfree = 0.000) for 6398 atoms. Found 23 (48 requested) and removed 34 (24 requested) atoms. Cycle 14: After refmac, R = 0.2051 (Rfree = 0.000) for 6367 atoms. Found 20 (48 requested) and removed 31 (24 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 6346 atoms. Found 18 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 6567 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6588 seeds are put forward Round 1: 401 peptides, 77 chains. Longest chain 12 peptides. Score 0.339 Round 2: 450 peptides, 75 chains. Longest chain 13 peptides. Score 0.433 Round 3: 462 peptides, 72 chains. Longest chain 16 peptides. Score 0.471 Round 4: 509 peptides, 71 chains. Longest chain 21 peptides. Score 0.544 Round 5: 490 peptides, 69 chains. Longest chain 24 peptides. Score 0.530 Taking the results from Round 4 Chains 73, Residues 438, Estimated correctness of the model 9.3 % 10 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14235 restraints for refining 6474 atoms. 12473 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2201 (Rfree = 0.000) for 6474 atoms. Found 29 (48 requested) and removed 38 (24 requested) atoms. Cycle 17: After refmac, R = 0.2149 (Rfree = 0.000) for 6442 atoms. Found 17 (48 requested) and removed 34 (24 requested) atoms. Cycle 18: After refmac, R = 0.2127 (Rfree = 0.000) for 6409 atoms. Found 32 (48 requested) and removed 26 (24 requested) atoms. Cycle 19: After refmac, R = 0.2121 (Rfree = 0.000) for 6404 atoms. Found 26 (48 requested) and removed 36 (24 requested) atoms. Cycle 20: After refmac, R = 0.2085 (Rfree = 0.000) for 6380 atoms. Found 13 (48 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 6574 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6598 seeds are put forward Round 1: 386 peptides, 76 chains. Longest chain 12 peptides. Score 0.320 Round 2: 433 peptides, 72 chains. Longest chain 15 peptides. Score 0.427 Round 3: 433 peptides, 68 chains. Longest chain 15 peptides. Score 0.454 Round 4: 428 peptides, 68 chains. Longest chain 15 peptides. Score 0.446 Round 5: 441 peptides, 65 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 5 Chains 65, Residues 376, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14836 restraints for refining 6472 atoms. 13362 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2257 (Rfree = 0.000) for 6472 atoms. Found 23 (48 requested) and removed 27 (24 requested) atoms. Cycle 22: After refmac, R = 0.2172 (Rfree = 0.000) for 6430 atoms. Found 30 (48 requested) and removed 32 (24 requested) atoms. Cycle 23: After refmac, R = 0.2180 (Rfree = 0.000) for 6407 atoms. Found 31 (48 requested) and removed 29 (24 requested) atoms. Cycle 24: After refmac, R = 0.2110 (Rfree = 0.000) for 6393 atoms. Found 39 (48 requested) and removed 31 (24 requested) atoms. Cycle 25: After refmac, R = 0.2029 (Rfree = 0.000) for 6393 atoms. Found 22 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 6563 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6589 seeds are put forward Round 1: 376 peptides, 72 chains. Longest chain 10 peptides. Score 0.332 Round 2: 434 peptides, 74 chains. Longest chain 16 peptides. Score 0.414 Round 3: 409 peptides, 67 chains. Longest chain 16 peptides. Score 0.423 Round 4: 430 peptides, 62 chains. Longest chain 34 peptides. Score 0.489 Round 5: 431 peptides, 62 chains. Longest chain 22 peptides. Score 0.490 Taking the results from Round 5 Chains 62, Residues 369, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14512 restraints for refining 6473 atoms. 12980 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2234 (Rfree = 0.000) for 6473 atoms. Found 41 (48 requested) and removed 36 (24 requested) atoms. Cycle 27: After refmac, R = 0.2142 (Rfree = 0.000) for 6457 atoms. Found 35 (48 requested) and removed 28 (24 requested) atoms. Cycle 28: After refmac, R = 0.2109 (Rfree = 0.000) for 6445 atoms. Found 34 (48 requested) and removed 32 (24 requested) atoms. Cycle 29: After refmac, R = 0.1861 (Rfree = 0.000) for 6431 atoms. Found 21 (48 requested) and removed 34 (24 requested) atoms. Cycle 30: After refmac, R = 0.1789 (Rfree = 0.000) for 6413 atoms. Found 13 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 6568 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6587 seeds are put forward Round 1: 359 peptides, 71 chains. Longest chain 11 peptides. Score 0.310 Round 2: 430 peptides, 76 chains. Longest chain 21 peptides. Score 0.394 Round 3: 434 peptides, 73 chains. Longest chain 20 peptides. Score 0.421 Round 4: 407 peptides, 65 chains. Longest chain 35 peptides. Score 0.434 Round 5: 412 peptides, 68 chains. Longest chain 25 peptides. Score 0.421 Taking the results from Round 4 Chains 67, Residues 342, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14528 restraints for refining 6473 atoms. 13102 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 6473 atoms. Found 31 (48 requested) and removed 27 (24 requested) atoms. Cycle 32: After refmac, R = 0.2097 (Rfree = 0.000) for 6449 atoms. Found 32 (48 requested) and removed 30 (24 requested) atoms. Cycle 33: After refmac, R = 0.2108 (Rfree = 0.000) for 6432 atoms. Found 35 (48 requested) and removed 29 (24 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 6427 atoms. Found 27 (48 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.1762 (Rfree = 0.000) for 6416 atoms. Found 12 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 6527 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6545 seeds are put forward Round 1: 335 peptides, 70 chains. Longest chain 11 peptides. Score 0.274 Round 2: 387 peptides, 72 chains. Longest chain 10 peptides. Score 0.351 Round 3: 402 peptides, 70 chains. Longest chain 21 peptides. Score 0.391 Round 4: 413 peptides, 70 chains. Longest chain 13 peptides. Score 0.408 Round 5: 402 peptides, 66 chains. Longest chain 18 peptides. Score 0.419 Taking the results from Round 5 Chains 68, Residues 336, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14840 restraints for refining 6472 atoms. 13482 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2103 (Rfree = 0.000) for 6472 atoms. Found 39 (48 requested) and removed 31 (24 requested) atoms. Cycle 37: After refmac, R = 0.2062 (Rfree = 0.000) for 6463 atoms. Found 40 (48 requested) and removed 25 (24 requested) atoms. Cycle 38: After refmac, R = 0.2008 (Rfree = 0.000) for 6454 atoms. Found 29 (48 requested) and removed 31 (24 requested) atoms. Cycle 39: After refmac, R = 0.1791 (Rfree = 0.000) for 6445 atoms. Found 5 (48 requested) and removed 27 (24 requested) atoms. Cycle 40: After refmac, R = 0.1719 (Rfree = 0.000) for 6420 atoms. Found 4 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 6583 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6596 seeds are put forward Round 1: 323 peptides, 68 chains. Longest chain 7 peptides. Score 0.267 Round 2: 363 peptides, 65 chains. Longest chain 25 peptides. Score 0.361 Round 3: 371 peptides, 65 chains. Longest chain 14 peptides. Score 0.375 Round 4: 358 peptides, 58 chains. Longest chain 25 peptides. Score 0.404 Round 5: 353 peptides, 60 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 59, Residues 300, Estimated correctness of the model 0.0 % 8 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12678 reflections ( 89.55 % complete ) and 14652 restraints for refining 6474 atoms. 13395 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2163 (Rfree = 0.000) for 6474 atoms. Found 37 (48 requested) and removed 29 (24 requested) atoms. Cycle 42: After refmac, R = 0.2122 (Rfree = 0.000) for 6468 atoms. Found 46 (48 requested) and removed 30 (24 requested) atoms. Cycle 43: After refmac, R = 0.1887 (Rfree = 0.000) for 6477 atoms. Found 20 (48 requested) and removed 39 (24 requested) atoms. Cycle 44: After refmac, R = 0.1848 (Rfree = 0.000) for 6450 atoms. Found 11 (48 requested) and removed 28 (24 requested) atoms. Cycle 45: After refmac, R = 0.1823 (Rfree = 0.000) for 6428 atoms. Found 9 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6557 seeds are put forward Round 1: 306 peptides, 68 chains. Longest chain 11 peptides. Score 0.235 Round 2: 346 peptides, 64 chains. Longest chain 17 peptides. Score 0.339 Round 3: 361 peptides, 66 chains. Longest chain 17 peptides. Score 0.350 Round 4: 359 peptides, 66 chains. Longest chain 12 peptides. Score 0.347 Round 5: 345 peptides, 64 chains. Longest chain 17 peptides. Score 0.337 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 295, Estimated correctness of the model 0.0 % 8 chains (29 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (295 residues) following loop building 8 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12678 reflections ( 89.55 % complete ) and 14993 restraints for refining 6474 atoms. 13821 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2171 (Rfree = 0.000) for 6474 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2249 (Rfree = 0.000) for 6441 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.2184 (Rfree = 0.000) for 6408 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.1912 (Rfree = 0.000) for 6378 atoms. Found 0 (48 requested) and removed 21 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:30:33 GMT 2018 Job finished. TimeTaking 62.66 Used memory is bytes: 5440584