Mon 24 Dec 00:12:32 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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 00:12:37 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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 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-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-3.4-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 3.400 Wilson plot Bfac: 70.40 89442 reflections ( 93.49 % complete ) and 0 restraints for refining 45416 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.2982 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2339 (Rfree = 0.000) for 45416 atoms. Found 342 (342 requested) and removed 222 (171 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 46584 seeds are put forward NCS extension: 0 residues added, 46584 seeds are put forward Round 1: 2976 peptides, 490 chains. Longest chain 31 peptides. Score 0.423 Round 2: 3398 peptides, 447 chains. Longest chain 34 peptides. Score 0.548 Round 3: 3516 peptides, 413 chains. Longest chain 46 peptides. Score 0.597 Round 4: 3591 peptides, 393 chains. Longest chain 31 peptides. Score 0.625 Round 5: 3625 peptides, 393 chains. Longest chain 49 peptides. Score 0.631 Taking the results from Round 5 Chains 424, Residues 3232, Estimated correctness of the model 38.5 % 35 chains (560 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14850 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2132 (Rfree = 0.000) for 37359 atoms. Found 231 (282 requested) and removed 218 (141 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.1962 (Rfree = 0.000) for 37372 atoms. Found 100 (282 requested) and removed 175 (141 requested) atoms. Cycle 3: After refmac, R = 0.1869 (Rfree = 0.000) for 37297 atoms. Found 78 (281 requested) and removed 171 (140 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1813 (Rfree = 0.000) for 37204 atoms. Found 87 (280 requested) and removed 153 (140 requested) atoms. Cycle 5: After refmac, R = 0.1772 (Rfree = 0.000) for 37138 atoms. Found 69 (280 requested) and removed 147 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 38469 seeds are put forward NCS extension: 0 residues added, 38469 seeds are put forward Round 1: 3322 peptides, 445 chains. Longest chain 36 peptides. Score 0.536 Round 2: 3617 peptides, 405 chains. Longest chain 39 peptides. Score 0.620 Round 3: 3637 peptides, 388 chains. Longest chain 42 peptides. Score 0.636 Round 4: 3601 peptides, 366 chains. Longest chain 44 peptides. Score 0.647 Round 5: 3635 peptides, 380 chains. Longest chain 37 peptides. Score 0.642 Taking the results from Round 4 Chains 396, Residues 3235, Estimated correctness of the model 43.3 % 32 chains (591 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 15084 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1989 (Rfree = 0.000) for 37359 atoms. Found 196 (282 requested) and removed 215 (141 requested) atoms. Cycle 7: After refmac, R = 0.1803 (Rfree = 0.000) for 37340 atoms. Found 71 (281 requested) and removed 161 (140 requested) atoms. Cycle 8: After refmac, R = 0.1764 (Rfree = 0.000) for 37250 atoms. Found 100 (281 requested) and removed 145 (140 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1706 (Rfree = 0.000) for 37205 atoms. Found 79 (280 requested) and removed 150 (140 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1680 (Rfree = 0.000) for 37134 atoms. Found 78 (280 requested) and removed 146 (140 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38370 seeds are put forward NCS extension: 17 residues added (16 deleted due to clashes), 38387 seeds are put forward Round 1: 3328 peptides, 426 chains. Longest chain 35 peptides. Score 0.553 Round 2: 3523 peptides, 390 chains. Longest chain 41 peptides. Score 0.616 Round 3: 3544 peptides, 383 chains. Longest chain 37 peptides. Score 0.625 Round 4: 3584 peptides, 384 chains. Longest chain 46 peptides. Score 0.631 Round 5: 3551 peptides, 382 chains. Longest chain 42 peptides. Score 0.627 Taking the results from Round 4 Chains 413, Residues 3200, Estimated correctness of the model 38.5 % 31 chains (465 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 14220 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1918 (Rfree = 0.000) for 37359 atoms. Found 264 (282 requested) and removed 209 (141 requested) atoms. Cycle 12: After refmac, R = 0.1756 (Rfree = 0.000) for 37414 atoms. Found 100 (282 requested) and removed 153 (141 requested) atoms. Cycle 13: After refmac, R = 0.1716 (Rfree = 0.000) for 37361 atoms. Found 71 (282 requested) and removed 148 (141 requested) atoms. Cycle 14: After refmac, R = 0.1668 (Rfree = 0.000) for 37284 atoms. Found 81 (281 requested) and removed 145 (140 requested) atoms. Cycle 15: After refmac, R = 0.1656 (Rfree = 0.000) for 37220 atoms. Found 70 (281 requested) and removed 147 (140 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38398 seeds are put forward NCS extension: 0 residues added, 38398 seeds are put forward Round 1: 3268 peptides, 426 chains. Longest chain 36 peptides. Score 0.542 Round 2: 3521 peptides, 402 chains. Longest chain 44 peptides. Score 0.607 Round 3: 3547 peptides, 385 chains. Longest chain 50 peptides. Score 0.624 Round 4: 3518 peptides, 396 chains. Longest chain 44 peptides. Score 0.611 Round 5: 3521 peptides, 395 chains. Longest chain 45 peptides. Score 0.612 Taking the results from Round 3 Chains 406, Residues 3162, Estimated correctness of the model 36.3 % 35 chains (584 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 14772 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1957 (Rfree = 0.000) for 37359 atoms. Found 221 (282 requested) and removed 197 (141 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1821 (Rfree = 0.000) for 37383 atoms. Found 98 (282 requested) and removed 158 (141 requested) atoms. Cycle 18: After refmac, R = 0.1806 (Rfree = 0.000) for 37323 atoms. Found 128 (281 requested) and removed 144 (140 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1755 (Rfree = 0.000) for 37307 atoms. Found 77 (281 requested) and removed 146 (140 requested) atoms. Cycle 20: After refmac, R = 0.1734 (Rfree = 0.000) for 37238 atoms. Found 80 (281 requested) and removed 149 (140 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38380 seeds are put forward NCS extension: 14 residues added (44 deleted due to clashes), 38394 seeds are put forward Round 1: 3221 peptides, 443 chains. Longest chain 27 peptides. Score 0.518 Round 2: 3432 peptides, 397 chains. Longest chain 34 peptides. Score 0.595 Round 3: 3450 peptides, 393 chains. Longest chain 48 peptides. Score 0.602 Round 4: 3456 peptides, 400 chains. Longest chain 34 peptides. Score 0.597 Round 5: 3412 peptides, 394 chains. Longest chain 31 peptides. Score 0.594 Taking the results from Round 3 Chains 411, Residues 3057, Estimated correctness of the model 29.3 % 33 chains (498 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 13921 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1925 (Rfree = 0.000) for 37359 atoms. Found 178 (282 requested) and removed 189 (141 requested) atoms. Cycle 22: After refmac, R = 0.1815 (Rfree = 0.000) for 37348 atoms. Found 88 (282 requested) and removed 152 (141 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1789 (Rfree = 0.000) for 37284 atoms. Found 118 (281 requested) and removed 144 (140 requested) atoms. Cycle 24: After refmac, R = 0.1748 (Rfree = 0.000) for 37258 atoms. Found 59 (281 requested) and removed 146 (140 requested) atoms. Cycle 25: After refmac, R = 0.1718 (Rfree = 0.000) for 37171 atoms. Found 56 (280 requested) and removed 144 (140 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38337 seeds are put forward NCS extension: 4 residues added (3 deleted due to clashes), 38341 seeds are put forward Round 1: 3087 peptides, 439 chains. Longest chain 27 peptides. Score 0.495 Round 2: 3347 peptides, 412 chains. Longest chain 45 peptides. Score 0.568 Round 3: 3359 peptides, 411 chains. Longest chain 35 peptides. Score 0.571 Round 4: 3387 peptides, 411 chains. Longest chain 34 peptides. Score 0.576 Round 5: 3338 peptides, 407 chains. Longest chain 40 peptides. Score 0.571 Taking the results from Round 4 Chains 427, Residues 2976, Estimated correctness of the model 20.7 % 25 chains (342 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 12860 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1922 (Rfree = 0.000) for 37359 atoms. Found 197 (282 requested) and removed 176 (141 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1810 (Rfree = 0.000) for 37380 atoms. Found 144 (282 requested) and removed 149 (141 requested) atoms. Cycle 28: After refmac, R = 0.1775 (Rfree = 0.000) for 37375 atoms. Found 129 (282 requested) and removed 151 (141 requested) atoms. Cycle 29: After refmac, R = 0.1752 (Rfree = 0.000) for 37353 atoms. Found 136 (282 requested) and removed 148 (141 requested) atoms. Cycle 30: After refmac, R = 0.1713 (Rfree = 0.000) for 37341 atoms. Found 107 (281 requested) and removed 148 (140 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38606 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 38616 seeds are put forward Round 1: 2950 peptides, 442 chains. Longest chain 23 peptides. Score 0.463 Round 2: 3286 peptides, 416 chains. Longest chain 36 peptides. Score 0.554 Round 3: 3302 peptides, 417 chains. Longest chain 31 peptides. Score 0.556 Round 4: 3308 peptides, 400 chains. Longest chain 38 peptides. Score 0.571 Round 5: 3231 peptides, 388 chains. Longest chain 31 peptides. Score 0.567 Taking the results from Round 4 Chains 411, Residues 2908, Estimated correctness of the model 18.9 % 25 chains (333 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 12614 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1868 (Rfree = 0.000) for 37359 atoms. Found 172 (282 requested) and removed 179 (141 requested) atoms. Cycle 32: After refmac, R = 0.1773 (Rfree = 0.000) for 37352 atoms. Found 89 (282 requested) and removed 151 (141 requested) atoms. Cycle 33: After refmac, R = 0.1762 (Rfree = 0.000) for 37290 atoms. Found 146 (281 requested) and removed 145 (140 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 37291 atoms. Found 99 (281 requested) and removed 147 (140 requested) atoms. Cycle 35: After refmac, R = 0.1689 (Rfree = 0.000) for 37243 atoms. Found 91 (281 requested) and removed 149 (140 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.86 Search for helices and strands: 0 residues in 0 chains, 38443 seeds are put forward NCS extension: 0 residues added, 38443 seeds are put forward Round 1: 2885 peptides, 447 chains. Longest chain 21 peptides. Score 0.445 Round 2: 3130 peptides, 423 chains. Longest chain 29 peptides. Score 0.518 Round 3: 3140 peptides, 410 chains. Longest chain 22 peptides. Score 0.531 Round 4: 3223 peptides, 417 chains. Longest chain 31 peptides. Score 0.541 Round 5: 3201 peptides, 393 chains. Longest chain 42 peptides. Score 0.557 Taking the results from Round 5 Chains 399, Residues 2808, Estimated correctness of the model 14.0 % 16 chains (234 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 11793 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1864 (Rfree = 0.000) for 37359 atoms. Found 199 (282 requested) and removed 184 (141 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1776 (Rfree = 0.000) for 37374 atoms. Found 149 (282 requested) and removed 151 (141 requested) atoms. Cycle 38: After refmac, R = 0.1744 (Rfree = 0.000) for 37372 atoms. Found 129 (282 requested) and removed 148 (141 requested) atoms. Cycle 39: After refmac, R = 0.1573 (Rfree = 0.000) for 37353 atoms. Found 26 (282 requested) and removed 144 (141 requested) atoms. Cycle 40: After refmac, R = 0.1591 (Rfree = 0.000) for 37235 atoms. Found 52 (281 requested) and removed 142 (140 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 38458 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 38484 seeds are put forward Round 1: 2777 peptides, 461 chains. Longest chain 21 peptides. Score 0.407 Round 2: 3047 peptides, 420 chains. Longest chain 24 peptides. Score 0.504 Round 3: 3119 peptides, 414 chains. Longest chain 31 peptides. Score 0.523 Round 4: 3080 peptides, 404 chains. Longest chain 23 peptides. Score 0.525 Round 5: 3144 peptides, 402 chains. Longest chain 40 peptides. Score 0.539 Taking the results from Round 5 Chains 413, Residues 2742, Estimated correctness of the model 7.5 % 23 chains (298 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 11831 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1866 (Rfree = 0.000) for 37359 atoms. Found 190 (282 requested) and removed 185 (141 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1767 (Rfree = 0.000) for 37364 atoms. Found 136 (282 requested) and removed 151 (141 requested) atoms. Cycle 43: After refmac, R = 0.1752 (Rfree = 0.000) for 37349 atoms. Found 149 (282 requested) and removed 152 (141 requested) atoms. Cycle 44: After refmac, R = 0.1715 (Rfree = 0.000) for 37346 atoms. Found 152 (281 requested) and removed 153 (140 requested) atoms. Cycle 45: After refmac, R = 0.1679 (Rfree = 0.000) for 37345 atoms. Found 142 (281 requested) and removed 152 (140 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38652 seeds are put forward NCS extension: 0 residues added, 38652 seeds are put forward Round 1: 2626 peptides, 424 chains. Longest chain 24 peptides. Score 0.409 Round 2: 2960 peptides, 406 chains. Longest chain 37 peptides. Score 0.499 Round 3: 2939 peptides, 400 chains. Longest chain 22 peptides. Score 0.500 Round 4: 3010 peptides, 398 chains. Longest chain 30 peptides. Score 0.516 Round 5: 3037 peptides, 402 chains. Longest chain 36 peptides. Score 0.518 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 414, Residues 2635, Estimated correctness of the model 0.0 % 19 chains (271 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 414 chains (2635 residues) following loop building 19 chains (271 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 11250 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1825 (Rfree = 0.000) for 37359 atoms. Found 0 (282 requested) and removed 83 (141 requested) atoms. Cycle 47: After refmac, R = 0.1763 (Rfree = 0.000) for 37276 atoms. Found 0 (281 requested) and removed 67 (140 requested) atoms. Cycle 48: After refmac, R = 0.1721 (Rfree = 0.000) for 37209 atoms. Found 0 (280 requested) and removed 124 (140 requested) atoms. Cycle 49: After refmac, R = 0.1639 (Rfree = 0.000) for 37085 atoms. Found 0 (280 requested) and removed 111 (140 requested) atoms. Writing output files ... TimeTaking 450.95