Mon 24 Dec 00:03:43 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 2pnk-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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/2pnk-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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 00:03:47 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/2pnk-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.2-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 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-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.2-parrot-mrncs.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 Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 0 restraints for refining 45349 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.2941 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2140 (Rfree = 0.000) for 45349 atoms. Found 377 (406 requested) and removed 250 (203 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 46549 seeds are put forward NCS extension: 0 residues added, 46549 seeds are put forward Round 1: 3322 peptides, 487 chains. Longest chain 23 peptides. Score 0.499 Round 2: 3726 peptides, 434 chains. Longest chain 33 peptides. Score 0.616 Round 3: 3824 peptides, 400 chains. Longest chain 37 peptides. Score 0.656 Round 4: 3886 peptides, 381 chains. Longest chain 46 peptides. Score 0.679 Round 5: 3921 peptides, 366 chains. Longest chain 47 peptides. Score 0.694 Taking the results from Round 5 Chains 395, Residues 3555, Estimated correctness of the model 63.9 % 55 chains (1089 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 18448 restraints for refining 38766 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2203 (Rfree = 0.000) for 38766 atoms. Found 323 (347 requested) and removed 275 (173 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.1972 (Rfree = 0.000) for 38814 atoms. Found 104 (348 requested) and removed 195 (174 requested) atoms. Cycle 3: After refmac, R = 0.1893 (Rfree = 0.000) for 38723 atoms. Found 60 (347 requested) and removed 189 (173 requested) atoms. Cycle 4: After refmac, R = 0.1859 (Rfree = 0.000) for 38594 atoms. Found 59 (346 requested) and removed 178 (173 requested) atoms. Cycle 5: After refmac, R = 0.1811 (Rfree = 0.000) for 38475 atoms. Found 56 (345 requested) and removed 174 (172 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 39563 seeds are put forward NCS extension: 23 residues added (25 deleted due to clashes), 39586 seeds are put forward Round 1: 3632 peptides, 406 chains. Longest chain 47 peptides. Score 0.622 Round 2: 3905 peptides, 374 chains. Longest chain 44 peptides. Score 0.686 Round 3: 3897 peptides, 366 chains. Longest chain 48 peptides. Score 0.690 Round 4: 3892 peptides, 346 chains. Longest chain 48 peptides. Score 0.703 Round 5: 3886 peptides, 358 chains. Longest chain 42 peptides. Score 0.694 Taking the results from Round 4 Chains 386, Residues 3546, Estimated correctness of the model 65.8 % 60 chains (1165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 185 F and 194 F Built loop between residues 151 I and 159 I Built loop between residues 233 I and 236 I Built loop between residues 227 L and 233 L 378 chains (3551 residues) following loop building 56 chains (1187 residues) in sequence following loop building ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 18842 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2215 (Rfree = 0.000) for 37512 atoms. Found 336 (336 requested) and removed 274 (168 requested) atoms. Cycle 7: After refmac, R = 0.1950 (Rfree = 0.000) for 37574 atoms. Found 103 (330 requested) and removed 187 (168 requested) atoms. Cycle 8: After refmac, R = 0.1866 (Rfree = 0.000) for 37490 atoms. Found 55 (323 requested) and removed 175 (168 requested) atoms. Cycle 9: After refmac, R = 0.1839 (Rfree = 0.000) for 37370 atoms. Found 72 (315 requested) and removed 172 (167 requested) atoms. Cycle 10: After refmac, R = 0.1787 (Rfree = 0.000) for 37270 atoms. Found 50 (307 requested) and removed 176 (167 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 38386 seeds are put forward NCS extension: 27 residues added (47 deleted due to clashes), 38413 seeds are put forward Round 1: 3663 peptides, 400 chains. Longest chain 48 peptides. Score 0.631 Round 2: 3822 peptides, 363 chains. Longest chain 49 peptides. Score 0.682 Round 3: 3829 peptides, 353 chains. Longest chain 50 peptides. Score 0.689 Round 4: 3843 peptides, 366 chains. Longest chain 54 peptides. Score 0.683 Round 5: 3877 peptides, 360 chains. Longest chain 51 peptides. Score 0.691 Taking the results from Round 5 Chains 396, Residues 3517, Estimated correctness of the model 63.2 % 54 chains (1115 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 18596 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2171 (Rfree = 0.000) for 37512 atoms. Found 302 (302 requested) and removed 261 (168 requested) atoms. Cycle 12: After refmac, R = 0.2009 (Rfree = 0.000) for 37553 atoms. Found 101 (303 requested) and removed 178 (168 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1883 (Rfree = 0.000) for 37476 atoms. Found 54 (302 requested) and removed 171 (168 requested) atoms. Cycle 14: After refmac, R = 0.1852 (Rfree = 0.000) for 37359 atoms. Found 53 (301 requested) and removed 175 (167 requested) atoms. Cycle 15: After refmac, R = 0.1821 (Rfree = 0.000) for 37237 atoms. Found 58 (301 requested) and removed 169 (167 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38298 seeds are put forward NCS extension: 6 residues added (10 deleted due to clashes), 38304 seeds are put forward Round 1: 3588 peptides, 421 chains. Longest chain 31 peptides. Score 0.603 Round 2: 3761 peptides, 369 chains. Longest chain 35 peptides. Score 0.669 Round 3: 3785 peptides, 382 chains. Longest chain 38 peptides. Score 0.663 Round 4: 3769 peptides, 372 chains. Longest chain 48 peptides. Score 0.668 Round 5: 3676 peptides, 370 chains. Longest chain 38 peptides. Score 0.655 Taking the results from Round 2 Chains 400, Residues 3392, Estimated correctness of the model 58.3 % 54 chains (989 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 17416 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2065 (Rfree = 0.000) for 37512 atoms. Found 277 (302 requested) and removed 245 (168 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1889 (Rfree = 0.000) for 37544 atoms. Found 66 (302 requested) and removed 174 (168 requested) atoms. Cycle 18: After refmac, R = 0.1844 (Rfree = 0.000) for 37436 atoms. Found 57 (301 requested) and removed 169 (167 requested) atoms. Cycle 19: After refmac, R = 0.1812 (Rfree = 0.000) for 37324 atoms. Found 56 (301 requested) and removed 171 (167 requested) atoms. Cycle 20: After refmac, R = 0.1775 (Rfree = 0.000) for 37209 atoms. Found 61 (300 requested) and removed 167 (166 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38203 seeds are put forward NCS extension: 10 residues added (13 deleted due to clashes), 38213 seeds are put forward Round 1: 3437 peptides, 415 chains. Longest chain 42 peptides. Score 0.582 Round 2: 3661 peptides, 372 chains. Longest chain 50 peptides. Score 0.652 Round 3: 3715 peptides, 380 chains. Longest chain 47 peptides. Score 0.654 Round 4: 3710 peptides, 356 chains. Longest chain 53 peptides. Score 0.670 Round 5: 3715 peptides, 368 chains. Longest chain 58 peptides. Score 0.663 Taking the results from Round 4 Chains 394, Residues 3354, Estimated correctness of the model 58.5 % 52 chains (962 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 107474 reflections ( 93.72 % complete ) and 17241 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2110 (Rfree = 0.000) for 37512 atoms. Found 260 (302 requested) and removed 268 (168 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1997 (Rfree = 0.000) for 37504 atoms. Found 85 (302 requested) and removed 178 (168 requested) atoms. Cycle 23: After refmac, R = 0.1863 (Rfree = 0.000) for 37411 atoms. Found 63 (301 requested) and removed 172 (167 requested) atoms. Cycle 24: After refmac, R = 0.1830 (Rfree = 0.000) for 37302 atoms. Found 57 (301 requested) and removed 168 (167 requested) atoms. Cycle 25: After refmac, R = 0.1814 (Rfree = 0.000) for 37191 atoms. Found 59 (300 requested) and removed 167 (166 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38205 seeds are put forward NCS extension: 0 residues added, 38205 seeds are put forward Round 1: 3381 peptides, 418 chains. Longest chain 40 peptides. Score 0.569 Round 2: 3718 peptides, 381 chains. Longest chain 38 peptides. Score 0.654 Round 3: 3672 peptides, 378 chains. Longest chain 50 peptides. Score 0.649 Round 4: 3698 peptides, 380 chains. Longest chain 48 peptides. Score 0.652 Round 5: 3684 peptides, 382 chains. Longest chain 47 peptides. Score 0.648 Taking the results from Round 2 Chains 406, Residues 3337, Estimated correctness of the model 54.8 % 47 chains (807 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 16578 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2057 (Rfree = 0.000) for 37512 atoms. Found 279 (302 requested) and removed 230 (168 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1901 (Rfree = 0.000) for 37561 atoms. Found 92 (303 requested) and removed 177 (168 requested) atoms. Cycle 28: After refmac, R = 0.1854 (Rfree = 0.000) for 37476 atoms. Found 96 (302 requested) and removed 171 (168 requested) atoms. Cycle 29: After refmac, R = 0.1806 (Rfree = 0.000) for 37401 atoms. Found 74 (301 requested) and removed 172 (167 requested) atoms. Cycle 30: After refmac, R = 0.1769 (Rfree = 0.000) for 37303 atoms. Found 55 (301 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, 38244 seeds are put forward NCS extension: 7 residues added (15 deleted due to clashes), 38251 seeds are put forward Round 1: 3291 peptides, 419 chains. Longest chain 32 peptides. Score 0.552 Round 2: 3546 peptides, 372 chains. Longest chain 41 peptides. Score 0.634 Round 3: 3567 peptides, 376 chains. Longest chain 41 peptides. Score 0.634 Round 4: 3547 peptides, 367 chains. Longest chain 51 peptides. Score 0.638 Round 5: 3526 peptides, 390 chains. Longest chain 51 peptides. Score 0.617 Taking the results from Round 4 Chains 394, Residues 3180, Estimated correctness of the model 50.9 % 39 chains (704 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 15434 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2023 (Rfree = 0.000) for 37512 atoms. Found 241 (302 requested) and removed 234 (168 requested) atoms. Cycle 32: After refmac, R = 0.1850 (Rfree = 0.000) for 37519 atoms. Found 69 (302 requested) and removed 171 (168 requested) atoms. Cycle 33: After refmac, R = 0.1816 (Rfree = 0.000) for 37417 atoms. Found 68 (301 requested) and removed 169 (167 requested) atoms. Cycle 34: After refmac, R = 0.1801 (Rfree = 0.000) for 37316 atoms. Found 57 (301 requested) and removed 169 (167 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1769 (Rfree = 0.000) for 37204 atoms. Found 56 (300 requested) and removed 168 (166 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 38155 seeds are put forward NCS extension: 11 residues added (17 deleted due to clashes), 38166 seeds are put forward Round 1: 3187 peptides, 418 chains. Longest chain 48 peptides. Score 0.533 Round 2: 3427 peptides, 382 chains. Longest chain 35 peptides. Score 0.606 Round 3: 3451 peptides, 389 chains. Longest chain 39 peptides. Score 0.605 Round 4: 3457 peptides, 387 chains. Longest chain 42 peptides. Score 0.608 Round 5: 3501 peptides, 389 chains. Longest chain 48 peptides. Score 0.613 Taking the results from Round 5 Chains 411, Residues 3112, Estimated correctness of the model 44.5 % 40 chains (654 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 14869 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2031 (Rfree = 0.000) for 37512 atoms. Found 251 (302 requested) and removed 228 (168 requested) atoms. Cycle 37: After refmac, R = 0.1846 (Rfree = 0.000) for 37535 atoms. Found 103 (302 requested) and removed 176 (168 requested) atoms. Cycle 38: After refmac, R = 0.1813 (Rfree = 0.000) for 37462 atoms. Found 78 (302 requested) and removed 170 (168 requested) atoms. Cycle 39: After refmac, R = 0.1791 (Rfree = 0.000) for 37370 atoms. Found 76 (301 requested) and removed 169 (167 requested) atoms. Cycle 40: After refmac, R = 0.1781 (Rfree = 0.000) for 37277 atoms. Found 66 (301 requested) and removed 167 (167 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38253 seeds are put forward NCS extension: 10 residues added (18 deleted due to clashes), 38263 seeds are put forward Round 1: 3099 peptides, 443 chains. Longest chain 39 peptides. Score 0.493 Round 2: 3366 peptides, 399 chains. Longest chain 41 peptides. Score 0.582 Round 3: 3394 peptides, 398 chains. Longest chain 39 peptides. Score 0.588 Round 4: 3477 peptides, 405 chains. Longest chain 43 peptides. Score 0.597 Round 5: 3373 peptides, 391 chains. Longest chain 47 peptides. Score 0.590 Taking the results from Round 4 Chains 425, Residues 3072, Estimated correctness of the model 40.2 % 32 chains (555 residues) have been docked in sequence ------------------------------------------------------ 107474 reflections ( 93.72 % complete ) and 14295 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1999 (Rfree = 0.000) for 37512 atoms. Found 246 (302 requested) and removed 217 (168 requested) atoms. Cycle 42: After refmac, R = 0.1844 (Rfree = 0.000) for 37541 atoms. Found 83 (302 requested) and removed 171 (168 requested) atoms. Cycle 43: After refmac, R = 0.1810 (Rfree = 0.000) for 37453 atoms. Found 63 (302 requested) and removed 168 (168 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1788 (Rfree = 0.000) for 37348 atoms. Found 64 (301 requested) and removed 167 (167 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1768 (Rfree = 0.000) for 37245 atoms. Found 64 (301 requested) and removed 168 (167 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 38151 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 38165 seeds are put forward Round 1: 2961 peptides, 431 chains. Longest chain 32 peptides. Score 0.476 Round 2: 3262 peptides, 386 chains. Longest chain 44 peptides. Score 0.574 Round 3: 3287 peptides, 391 chains. Longest chain 38 peptides. Score 0.575 Round 4: 3241 peptides, 376 chains. Longest chain 38 peptides. Score 0.579 Round 5: 3216 peptides, 364 chains. Longest chain 37 peptides. Score 0.584 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 385, Residues 2852, Estimated correctness of the model 36.7 % 33 chains (579 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 152 F and 163 F Built loop between residues 230 J and 233 J 383 chains (2847 residues) following loop building 31 chains (591 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 107474 reflections ( 93.72 % complete ) and 13325 restraints for refining 37512 atoms. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2038 (Rfree = 0.000) for 37512 atoms. Found 0 (302 requested) and removed 74 (168 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1928 (Rfree = 0.000) for 37438 atoms. Found 0 (301 requested) and removed 40 (167 requested) atoms. Cycle 48: After refmac, R = 0.1907 (Rfree = 0.000) for 37398 atoms. Found 0 (301 requested) and removed 62 (167 requested) atoms. Cycle 49: After refmac, R = 0.1861 (Rfree = 0.000) for 37336 atoms. Found 0 (301 requested) and removed 64 (167 requested) atoms. Writing output files ... TimeTaking 410.97