Tue 25 Dec 19:27:55 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 2pnk-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-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/2pnk-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-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 ============================================================ Tue 25 Dec 19:28:05 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/2pnk-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-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 4739 and 0 Target number of residues in the AU: 4739 Target solvent content: 0.6371 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-3.4-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 70.40 89442 reflections ( 93.49 % complete ) and 0 restraints for refining 45363 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.2999 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2345 (Rfree = 0.000) for 45363 atoms. Found 342 (342 requested) and removed 233 (171 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 46539 seeds are put forward NCS extension: 0 residues added, 46539 seeds are put forward Round 1: 3006 peptides, 480 chains. Longest chain 21 peptides. Score 0.439 Round 2: 3447 peptides, 442 chains. Longest chain 39 peptides. Score 0.562 Round 3: 3580 peptides, 414 chains. Longest chain 40 peptides. Score 0.607 Round 4: 3645 peptides, 392 chains. Longest chain 50 peptides. Score 0.635 Round 5: 3643 peptides, 379 chains. Longest chain 34 peptides. Score 0.644 Taking the results from Round 5 Chains 400, Residues 3264, Estimated correctness of the model 42.4 % 32 chains (489 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 14752 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2094 (Rfree = 0.000) for 37359 atoms. Found 246 (282 requested) and removed 214 (141 requested) atoms. Cycle 2: After refmac, R = 0.1928 (Rfree = 0.000) for 37391 atoms. Found 114 (282 requested) and removed 160 (141 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 3: After refmac, R = 0.1862 (Rfree = 0.000) for 37345 atoms. Found 102 (281 requested) and removed 164 (140 requested) atoms. Cycle 4: After refmac, R = 0.1806 (Rfree = 0.000) for 37283 atoms. Found 86 (281 requested) and removed 157 (140 requested) atoms. Cycle 5: After refmac, R = 0.1761 (Rfree = 0.000) for 37212 atoms. Found 87 (280 requested) and removed 162 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38443 seeds are put forward NCS extension: 1 residues added (15 deleted due to clashes), 38444 seeds are put forward Round 1: 3359 peptides, 415 chains. Longest chain 33 peptides. Score 0.568 Round 2: 3599 peptides, 395 chains. Longest chain 33 peptides. Score 0.625 Round 3: 3646 peptides, 381 chains. Longest chain 41 peptides. Score 0.643 Round 4: 3622 peptides, 385 chains. Longest chain 50 peptides. Score 0.636 Round 5: 3600 peptides, 374 chains. Longest chain 59 peptides. Score 0.641 Taking the results from Round 3 Chains 402, Residues 3265, Estimated correctness of the model 42.1 % 31 chains (465 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14579 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1949 (Rfree = 0.000) for 37359 atoms. Found 215 (282 requested) and removed 192 (141 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1776 (Rfree = 0.000) for 37382 atoms. Found 93 (282 requested) and removed 153 (141 requested) atoms. Cycle 8: After refmac, R = 0.1748 (Rfree = 0.000) for 37322 atoms. Found 93 (281 requested) and removed 150 (140 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1680 (Rfree = 0.000) for 37265 atoms. Failed to save intermediate PDB Found 79 (281 requested) and removed 150 (140 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1654 (Rfree = 0.000) for 37194 atoms. Found 59 (280 requested) and removed 147 (140 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38390 seeds are put forward NCS extension: 19 residues added (22 deleted due to clashes), 38409 seeds are put forward Round 1: 3340 peptides, 427 chains. Longest chain 29 peptides. Score 0.554 Round 2: 3621 peptides, 400 chains. Longest chain 47 peptides. Score 0.625 Round 3: 3621 peptides, 394 chains. Longest chain 45 peptides. Score 0.629 Round 4: 3643 peptides, 388 chains. Longest chain 62 peptides. Score 0.637 Round 5: 3557 peptides, 366 chains. Longest chain 50 peptides. Score 0.640 Taking the results from Round 5 Chains 391, Residues 3191, Estimated correctness of the model 41.2 % 33 chains (544 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 14680 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1950 (Rfree = 0.000) for 37359 atoms. Found 214 (282 requested) and removed 204 (141 requested) atoms. Cycle 12: After refmac, R = 0.1800 (Rfree = 0.000) for 37369 atoms. Found 103 (282 requested) and removed 150 (141 requested) atoms. Cycle 13: After refmac, R = 0.1728 (Rfree = 0.000) for 37322 atoms. Found 75 (281 requested) and removed 148 (140 requested) atoms. Cycle 14: After refmac, R = 0.1681 (Rfree = 0.000) for 37249 atoms. Found 75 (281 requested) and removed 145 (140 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1637 (Rfree = 0.000) for 37179 atoms. Failed to save intermediate PDB Found 94 (280 requested) and removed 146 (140 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38427 seeds are put forward NCS extension: 14 residues added (17 deleted due to clashes), 38441 seeds are put forward Round 1: 3317 peptides, 439 chains. Longest chain 35 peptides. Score 0.540 Round 2: 3528 peptides, 389 chains. Longest chain 40 peptides. Score 0.618 Round 3: 3586 peptides, 382 chains. Longest chain 38 peptides. Score 0.633 Round 4: 3543 peptides, 372 chains. Longest chain 40 peptides. Score 0.633 Round 5: 3537 peptides, 376 chains. Longest chain 41 peptides. Score 0.629 Taking the results from Round 4 Chains 395, Residues 3171, Estimated correctness of the model 39.1 % 32 chains (540 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14593 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1925 (Rfree = 0.000) for 37359 atoms. Found 212 (282 requested) and removed 205 (141 requested) atoms. Cycle 17: After refmac, R = 0.1791 (Rfree = 0.000) for 37366 atoms. Found 115 (282 requested) and removed 146 (141 requested) atoms. Cycle 18: After refmac, R = 0.1748 (Rfree = 0.000) for 37335 atoms. Found 103 (281 requested) and removed 148 (140 requested) atoms. Cycle 19: After refmac, R = 0.1706 (Rfree = 0.000) for 37290 atoms. Found 97 (281 requested) and removed 147 (140 requested) atoms. Cycle 20: After refmac, R = 0.1673 (Rfree = 0.000) for 37240 atoms. Found 85 (281 requested) and removed 148 (140 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38437 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 38451 seeds are put forward Round 1: 3217 peptides, 420 chains. Longest chain 35 peptides. Score 0.537 Round 2: 3438 peptides, 392 chains. Longest chain 48 peptides. Score 0.600 Round 3: 3420 peptides, 387 chains. Longest chain 34 peptides. Score 0.601 Round 4: 3456 peptides, 394 chains. Longest chain 40 peptides. Score 0.602 Round 5: 3436 peptides, 385 chains. Longest chain 34 peptides. Score 0.606 Taking the results from Round 5 Chains 406, Residues 3051, Estimated correctness of the model 30.6 % 29 chains (477 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 13858 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1909 (Rfree = 0.000) for 37359 atoms. Found 207 (282 requested) and removed 180 (141 requested) atoms. Cycle 22: After refmac, R = 0.1768 (Rfree = 0.000) for 37386 atoms. Found 87 (282 requested) and removed 156 (141 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1716 (Rfree = 0.000) for 37317 atoms. Found 87 (281 requested) and removed 143 (140 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1688 (Rfree = 0.000) for 37261 atoms. Found 74 (281 requested) and removed 147 (140 requested) atoms. Cycle 25: After refmac, R = 0.1634 (Rfree = 0.000) for 37188 atoms. Found 73 (280 requested) and removed 147 (140 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.86 Search for helices and strands: 0 residues in 0 chains, 38385 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 38394 seeds are put forward Round 1: 3079 peptides, 445 chains. Longest chain 21 peptides. Score 0.487 Round 2: 3400 peptides, 410 chains. Longest chain 33 peptides. Score 0.579 Round 3: 3404 peptides, 402 chains. Longest chain 34 peptides. Score 0.586 Round 4: 3401 peptides, 396 chains. Longest chain 34 peptides. Score 0.591 Round 5: 3344 peptides, 383 chains. Longest chain 30 peptides. Score 0.591 Taking the results from Round 5 Chains 399, Residues 2961, Estimated correctness of the model 25.7 % 26 chains (334 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 12858 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1876 (Rfree = 0.000) for 37359 atoms. Found 192 (282 requested) and removed 189 (141 requested) atoms. Cycle 27: After refmac, R = 0.1730 (Rfree = 0.000) for 37362 atoms. Found 115 (282 requested) and removed 148 (141 requested) atoms. Cycle 28: After refmac, R = 0.1698 (Rfree = 0.000) for 37329 atoms. Found 120 (281 requested) and removed 142 (140 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1640 (Rfree = 0.000) for 37307 atoms. Found 84 (281 requested) and removed 143 (140 requested) atoms. Cycle 30: After refmac, R = 0.1614 (Rfree = 0.000) for 37248 atoms. Found 97 (281 requested) and removed 140 (140 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38451 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 38467 seeds are put forward Round 1: 2940 peptides, 434 chains. Longest chain 35 peptides. Score 0.469 Round 2: 3277 peptides, 388 chains. Longest chain 42 peptides. Score 0.575 Round 3: 3255 peptides, 396 chains. Longest chain 32 peptides. Score 0.565 Round 4: 3256 peptides, 391 chains. Longest chain 29 peptides. Score 0.569 Round 5: 3233 peptides, 388 chains. Longest chain 40 peptides. Score 0.567 Taking the results from Round 2 Chains 410, Residues 2889, Estimated correctness of the model 20.3 % 30 chains (389 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 12885 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1812 (Rfree = 0.000) for 37359 atoms. Found 186 (282 requested) and removed 193 (141 requested) atoms. Cycle 32: After refmac, R = 0.1727 (Rfree = 0.000) for 37352 atoms. Found 115 (282 requested) and removed 153 (141 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1675 (Rfree = 0.000) for 37314 atoms. Found 95 (281 requested) and removed 146 (140 requested) atoms. Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 37263 atoms. Found 125 (281 requested) and removed 145 (140 requested) atoms. Cycle 35: After refmac, R = 0.1510 (Rfree = 0.000) for 37243 atoms. Found 25 (281 requested) and removed 146 (140 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38321 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 38339 seeds are put forward Round 1: 2931 peptides, 441 chains. Longest chain 24 peptides. Score 0.460 Round 2: 3192 peptides, 426 chains. Longest chain 31 peptides. Score 0.527 Round 3: 3228 peptides, 420 chains. Longest chain 24 peptides. Score 0.539 Round 4: 3176 peptides, 396 chains. Longest chain 37 peptides. Score 0.550 Round 5: 3211 peptides, 396 chains. Longest chain 32 peptides. Score 0.557 Taking the results from Round 5 Chains 406, Residues 2815, Estimated correctness of the model 14.0 % 21 chains (318 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 12199 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1812 (Rfree = 0.000) for 37359 atoms. Found 190 (282 requested) and removed 183 (141 requested) atoms. Cycle 37: After refmac, R = 0.1691 (Rfree = 0.000) for 37366 atoms. Found 110 (282 requested) and removed 156 (141 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1679 (Rfree = 0.000) for 37320 atoms. Found 151 (281 requested) and removed 147 (140 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1623 (Rfree = 0.000) for 37324 atoms. Found 100 (281 requested) and removed 148 (140 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1476 (Rfree = 0.000) for 37276 atoms. Found 27 (281 requested) and removed 143 (140 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38410 seeds are put forward NCS extension: 4 residues added (11 deleted due to clashes), 38414 seeds are put forward Round 1: 2812 peptides, 437 chains. Longest chain 24 peptides. Score 0.438 Round 2: 3105 peptides, 415 chains. Longest chain 35 peptides. Score 0.520 Round 3: 3174 peptides, 404 chains. Longest chain 43 peptides. Score 0.543 Round 4: 3119 peptides, 391 chains. Longest chain 40 peptides. Score 0.544 Round 5: 3140 peptides, 394 chains. Longest chain 43 peptides. Score 0.545 Taking the results from Round 5 Chains 409, Residues 2746, Estimated correctness of the model 9.7 % 19 chains (274 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 11716 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1828 (Rfree = 0.000) for 37359 atoms. Found 191 (282 requested) and removed 182 (141 requested) atoms. Cycle 42: After refmac, R = 0.1719 (Rfree = 0.000) for 37368 atoms. Found 119 (282 requested) and removed 153 (141 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1697 (Rfree = 0.000) for 37334 atoms. Found 123 (281 requested) and removed 150 (140 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1540 (Rfree = 0.000) for 37307 atoms. Found 29 (281 requested) and removed 146 (140 requested) atoms. Cycle 45: After refmac, R = 0.1498 (Rfree = 0.000) for 37190 atoms. Found 27 (280 requested) and removed 141 (140 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.90 Search for helices and strands: 0 residues in 0 chains, 38270 seeds are put forward NCS extension: 12 residues added (12 deleted due to clashes), 38282 seeds are put forward Round 1: 2701 peptides, 435 chains. Longest chain 22 peptides. Score 0.415 Round 2: 2982 peptides, 410 chains. Longest chain 33 peptides. Score 0.500 Round 3: 3024 peptides, 399 chains. Longest chain 33 peptides. Score 0.518 Round 4: 3005 peptides, 405 chains. Longest chain 35 peptides. Score 0.509 Round 5: 3041 peptides, 388 chains. Longest chain 34 peptides. Score 0.531 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 400, Residues 2653, Estimated correctness of the model 4.6 % 19 chains (280 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 400 chains (2653 residues) following loop building 19 chains (280 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 11436 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1823 (Rfree = 0.000) for 37359 atoms. Found 0 (282 requested) and removed 98 (141 requested) atoms. Cycle 47: After refmac, R = 0.1754 (Rfree = 0.000) for 37261 atoms. Found 0 (281 requested) and removed 60 (140 requested) atoms. Cycle 48: After refmac, R = 0.1719 (Rfree = 0.000) for 37201 atoms. Found 0 (280 requested) and removed 104 (140 requested) atoms. Cycle 49: After refmac, R = 0.1676 (Rfree = 0.000) for 37097 atoms. TimeTaking 459.92