null Mon 24 Dec 07:44:23 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 2pnk-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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/2pnk-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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 07:44:28 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/2pnk-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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 4893 and 0 Target number of residues in the AU: 4893 Target solvent content: 0.6253 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-3.2-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: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 0.95 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. 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: 162.857 3.200 Wilson plot Bfac: 64.11 107474 reflections ( 93.72 % complete ) and 0 restraints for refining 45742 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.2970 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2281 (Rfree = 0.000) for 45742 atoms. Found 410 (410 requested) and removed 262 (205 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 46951 seeds are put forward NCS extension: 0 residues added, 46951 seeds are put forward Round 1: 3196 peptides, 498 chains. Longest chain 25 peptides. Score 0.463 Round 2: 3564 peptides, 434 chains. Longest chain 33 peptides. Score 0.589 Round 3: 3670 peptides, 407 chains. Longest chain 42 peptides. Score 0.627 Round 4: 3789 peptides, 393 chains. Longest chain 38 peptides. Score 0.656 Round 5: 3775 peptides, 372 chains. Longest chain 47 peptides. Score 0.669 Taking the results from Round 5 Chains 395, Residues 3403, Estimated correctness of the model 58.3 % 40 chains (794 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 16663 restraints for refining 38466 atoms. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2220 (Rfree = 0.000) for 38466 atoms. Found 340 (345 requested) and removed 262 (172 requested) atoms. Cycle 2: After refmac, R = 0.2000 (Rfree = 0.000) for 38544 atoms. Found 112 (345 requested) and removed 181 (172 requested) atoms. Cycle 3: After refmac, R = 0.1913 (Rfree = 0.000) for 38475 atoms. Found 64 (345 requested) and removed 180 (172 requested) atoms. Cycle 4: After refmac, R = 0.1856 (Rfree = 0.000) for 38359 atoms. Found 48 (344 requested) and removed 176 (172 requested) atoms. Cycle 5: After refmac, R = 0.1804 (Rfree = 0.000) for 38231 atoms. Found 49 (343 requested) and removed 173 (171 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 39278 seeds are put forward NCS extension: 0 residues added, 39278 seeds are put forward Round 1: 3549 peptides, 412 chains. Longest chain 37 peptides. Score 0.604 Round 2: 3832 peptides, 385 chains. Longest chain 45 peptides. Score 0.668 Round 3: 3841 peptides, 349 chains. Longest chain 51 peptides. Score 0.694 Round 4: 3821 peptides, 375 chains. Longest chain 71 peptides. Score 0.673 Round 5: 3821 peptides, 364 chains. Longest chain 50 peptides. Score 0.681 Taking the results from Round 3 Chains 374, Residues 3492, Estimated correctness of the model 63.9 % 50 chains (962 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 17723 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2141 (Rfree = 0.000) for 37512 atoms. Found 282 (336 requested) and removed 282 (168 requested) atoms. Cycle 7: After refmac, R = 0.1939 (Rfree = 0.000) for 37512 atoms. Found 95 (336 requested) and removed 180 (168 requested) atoms. Cycle 8: After refmac, R = 0.1882 (Rfree = 0.000) for 37427 atoms. Found 51 (335 requested) and removed 168 (167 requested) atoms. Cycle 9: After refmac, R = 0.1856 (Rfree = 0.000) for 37310 atoms. Found 62 (334 requested) and removed 169 (167 requested) atoms. Cycle 10: After refmac, R = 0.1833 (Rfree = 0.000) for 37203 atoms. Found 61 (333 requested) and removed 168 (166 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38227 seeds are put forward NCS extension: 18 residues added (30 deleted due to clashes), 38245 seeds are put forward Round 1: 3585 peptides, 414 chains. Longest chain 41 peptides. Score 0.608 Round 2: 3827 peptides, 365 chains. Longest chain 41 peptides. Score 0.681 Round 3: 3783 peptides, 361 chains. Longest chain 46 peptides. Score 0.678 Round 4: 3738 peptides, 372 chains. Longest chain 41 peptides. Score 0.663 Round 5: 3733 peptides, 363 chains. Longest chain 49 peptides. Score 0.669 Taking the results from Round 2 Chains 395, Residues 3462, Estimated correctness of the model 61.0 % 46 chains (872 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 17192 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 37512 atoms. Found 255 (336 requested) and removed 241 (168 requested) atoms. Cycle 12: After refmac, R = 0.1909 (Rfree = 0.000) for 37526 atoms. Found 72 (336 requested) and removed 174 (168 requested) atoms. Cycle 13: After refmac, R = 0.1873 (Rfree = 0.000) for 37424 atoms. Found 76 (335 requested) and removed 169 (167 requested) atoms. Cycle 14: After refmac, R = 0.1840 (Rfree = 0.000) for 37331 atoms. Found 73 (335 requested) and removed 169 (167 requested) atoms. Cycle 15: After refmac, R = 0.1805 (Rfree = 0.000) for 37235 atoms. Found 64 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38255 seeds are put forward NCS extension: 26 residues added (7 deleted due to clashes), 38281 seeds are put forward Round 1: 3512 peptides, 413 chains. Longest chain 48 peptides. Score 0.596 Round 2: 3772 peptides, 373 chains. Longest chain 41 peptides. Score 0.668 Round 3: 3762 peptides, 371 chains. Longest chain 50 peptides. Score 0.668 Round 4: 3789 peptides, 373 chains. Longest chain 41 peptides. Score 0.670 Round 5: 3786 peptides, 383 chains. Longest chain 46 peptides. Score 0.663 Taking the results from Round 4 Chains 400, Residues 3416, Estimated correctness of the model 58.5 % 50 chains (923 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 17217 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2129 (Rfree = 0.000) for 37512 atoms. Found 327 (336 requested) and removed 239 (168 requested) atoms. Cycle 17: After refmac, R = 0.1942 (Rfree = 0.000) for 37600 atoms. Found 87 (337 requested) and removed 176 (168 requested) atoms. Cycle 18: After refmac, R = 0.1881 (Rfree = 0.000) for 37511 atoms. Found 79 (336 requested) and removed 172 (168 requested) atoms. Cycle 19: After refmac, R = 0.1853 (Rfree = 0.000) for 37418 atoms. Found 69 (335 requested) and removed 170 (167 requested) atoms. Cycle 20: After refmac, R = 0.1821 (Rfree = 0.000) for 37317 atoms. Found 57 (334 requested) and removed 169 (167 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38410 seeds are put forward NCS extension: 13 residues added (12 deleted due to clashes), 38423 seeds are put forward Round 1: 3406 peptides, 407 chains. Longest chain 41 peptides. Score 0.583 Round 2: 3695 peptides, 371 chains. Longest chain 48 peptides. Score 0.658 Round 3: 3645 peptides, 375 chains. Longest chain 36 peptides. Score 0.647 Round 4: 3646 peptides, 378 chains. Longest chain 60 peptides. Score 0.645 Round 5: 3634 peptides, 387 chains. Longest chain 43 peptides. Score 0.636 Taking the results from Round 2 Chains 394, Residues 3324, Estimated correctness of the model 55.7 % 47 chains (882 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 16754 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2064 (Rfree = 0.000) for 37512 atoms. Found 310 (336 requested) and removed 268 (168 requested) atoms. Cycle 22: After refmac, R = 0.1909 (Rfree = 0.000) for 37554 atoms. Found 68 (337 requested) and removed 172 (168 requested) atoms. Cycle 23: After refmac, R = 0.1885 (Rfree = 0.000) for 37450 atoms. Found 64 (336 requested) and removed 168 (168 requested) atoms. Cycle 24: After refmac, R = 0.1857 (Rfree = 0.000) for 37346 atoms. Found 71 (335 requested) and removed 168 (167 requested) atoms. Cycle 25: After refmac, R = 0.1831 (Rfree = 0.000) for 37249 atoms. Found 39 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38222 seeds are put forward NCS extension: 3 residues added (9 deleted due to clashes), 38225 seeds are put forward Round 1: 3410 peptides, 406 chains. Longest chain 50 peptides. Score 0.584 Round 2: 3612 peptides, 379 chains. Longest chain 51 peptides. Score 0.639 Round 3: 3603 peptides, 391 chains. Longest chain 44 peptides. Score 0.629 Round 4: 3635 peptides, 378 chains. Longest chain 36 peptides. Score 0.643 Round 5: 3609 peptides, 393 chains. Longest chain 43 peptides. Score 0.628 Taking the results from Round 4 Chains 396, Residues 3257, Estimated correctness of the model 52.1 % 48 chains (894 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 16509 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 37512 atoms. Found 251 (336 requested) and removed 236 (168 requested) atoms. Cycle 27: After refmac, R = 0.1915 (Rfree = 0.000) for 37527 atoms. Found 88 (336 requested) and removed 175 (168 requested) atoms. Cycle 28: After refmac, R = 0.1882 (Rfree = 0.000) for 37440 atoms. Found 61 (336 requested) and removed 172 (168 requested) atoms. Cycle 29: After refmac, R = 0.1868 (Rfree = 0.000) for 37329 atoms. Found 63 (335 requested) and removed 171 (167 requested) atoms. Cycle 30: After refmac, R = 0.1837 (Rfree = 0.000) for 37221 atoms. Found 43 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38166 seeds are put forward NCS extension: 8 residues added (11 deleted due to clashes), 38174 seeds are put forward Round 1: 3333 peptides, 430 chains. Longest chain 35 peptides. Score 0.551 Round 2: 3545 peptides, 384 chains. Longest chain 47 peptides. Score 0.624 Round 3: 3562 peptides, 383 chains. Longest chain 51 peptides. Score 0.628 Round 4: 3555 peptides, 395 chains. Longest chain 44 peptides. Score 0.618 Round 5: 3504 peptides, 381 chains. Longest chain 54 peptides. Score 0.620 Taking the results from Round 3 Chains 403, Residues 3179, Estimated correctness of the model 48.4 % 31 chains (608 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 14967 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 37512 atoms. Found 336 (336 requested) and removed 219 (168 requested) atoms. Cycle 32: After refmac, R = 0.1953 (Rfree = 0.000) for 37629 atoms. Found 86 (337 requested) and removed 170 (168 requested) atoms. Cycle 33: After refmac, R = 0.1925 (Rfree = 0.000) for 37545 atoms. Found 94 (336 requested) and removed 169 (168 requested) atoms. Cycle 34: After refmac, R = 0.1892 (Rfree = 0.000) for 37470 atoms. Found 83 (336 requested) and removed 172 (168 requested) atoms. Cycle 35: After refmac, R = 0.1880 (Rfree = 0.000) for 37381 atoms. Found 60 (335 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 38349 seeds are put forward NCS extension: 28 residues added (15 deleted due to clashes), 38377 seeds are put forward Round 1: 3174 peptides, 428 chains. Longest chain 29 peptides. Score 0.522 Round 2: 3465 peptides, 404 chains. Longest chain 51 peptides. Score 0.595 Round 3: 3478 peptides, 405 chains. Longest chain 44 peptides. Score 0.597 Round 4: 3522 peptides, 385 chains. Longest chain 48 peptides. Score 0.620 Round 5: 3433 peptides, 398 chains. Longest chain 38 peptides. Score 0.595 Taking the results from Round 4 Chains 399, Residues 3137, Estimated correctness of the model 46.3 % 34 chains (642 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 14989 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 37512 atoms. Found 269 (336 requested) and removed 242 (168 requested) atoms. Cycle 37: After refmac, R = 0.1937 (Rfree = 0.000) for 37539 atoms. Found 92 (336 requested) and removed 177 (168 requested) atoms. Cycle 38: After refmac, R = 0.1901 (Rfree = 0.000) for 37454 atoms. Found 72 (336 requested) and removed 171 (168 requested) atoms. Cycle 39: After refmac, R = 0.1860 (Rfree = 0.000) for 37355 atoms. Found 68 (335 requested) and removed 169 (167 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 37254 atoms. Found 57 (334 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38297 seeds are put forward NCS extension: 0 residues added, 38297 seeds are put forward Round 1: 3120 peptides, 440 chains. Longest chain 37 peptides. Score 0.500 Round 2: 3426 peptides, 402 chains. Longest chain 51 peptides. Score 0.590 Round 3: 3378 peptides, 403 chains. Longest chain 47 peptides. Score 0.581 Round 4: 3361 peptides, 392 chains. Longest chain 40 peptides. Score 0.587 Round 5: 3375 peptides, 402 chains. Longest chain 48 peptides. Score 0.581 Taking the results from Round 2 Chains 415, Residues 3024, Estimated correctness of the model 38.3 % 28 chains (455 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 13618 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1961 (Rfree = 0.000) for 37512 atoms. Found 198 (336 requested) and removed 226 (168 requested) atoms. Cycle 42: After refmac, R = 0.1884 (Rfree = 0.000) for 37484 atoms. Found 93 (336 requested) and removed 173 (168 requested) atoms. Cycle 43: After refmac, R = 0.1834 (Rfree = 0.000) for 37404 atoms. Found 71 (335 requested) and removed 173 (167 requested) atoms. Cycle 44: After refmac, R = 0.1810 (Rfree = 0.000) for 37302 atoms. Found 63 (334 requested) and removed 169 (167 requested) atoms. Cycle 45: After refmac, R = 0.1788 (Rfree = 0.000) for 37196 atoms. Found 67 (333 requested) and removed 168 (166 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 38183 seeds are put forward NCS extension: 20 residues added (22 deleted due to clashes), 38203 seeds are put forward Round 1: 2948 peptides, 419 chains. Longest chain 30 peptides. Score 0.484 Round 2: 3271 peptides, 417 chains. Longest chain 34 peptides. Score 0.550 Round 3: 3272 peptides, 400 chains. Longest chain 36 peptides. Score 0.564 Round 4: 3276 peptides, 390 chains. Longest chain 33 peptides. Score 0.574 Round 5: 3300 peptides, 397 chains. Longest chain 33 peptides. Score 0.572 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 413, Residues 2886, Estimated correctness of the model 33.9 % 33 chains (495 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 307 G and 319 G Built loop between residues 159 J and 163 J 411 chains (2894 residues) following loop building 31 chains (509 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 107474 reflections ( 93.72 % complete ) and 13154 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2011 (Rfree = 0.000) for 37512 atoms. Found 0 (336 requested) and removed 77 (168 requested) atoms. Cycle 47: After refmac, R = 0.1920 (Rfree = 0.000) for 37435 atoms. Found 0 (335 requested) and removed 73 (167 requested) atoms. Cycle 48: After refmac, R = 0.1913 (Rfree = 0.000) for 37362 atoms. Found 0 (335 requested) and removed 64 (167 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 37298 atoms. Found 0 (334 requested) and removed 77 (167 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 14:37:47 GMT 2018 Job finished. TimeTaking 413.4 Used memory is bytes: 18348768