Mon 24 Dec 00:57:09 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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 00:57:14 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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 4628 and 0 Target number of residues in the AU: 4628 Target solvent content: 0.6456 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 75.44 Failed to save intermediate PDB 75179 reflections ( 93.20 % complete ) and 0 restraints for refining 45595 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3084 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2612 (Rfree = 0.000) for 45595 atoms. Found 292 (292 requested) and removed 221 (146 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 46795 seeds are put forward NCS extension: 0 residues added, 46795 seeds are put forward Round 1: 2823 peptides, 471 chains. Longest chain 19 peptides. Score 0.408 Round 2: 3251 peptides, 420 chains. Longest chain 30 peptides. Score 0.544 Round 3: 3309 peptides, 396 chains. Longest chain 37 peptides. Score 0.575 Round 4: 3401 peptides, 381 chains. Longest chain 43 peptides. Score 0.603 Round 5: 3368 peptides, 378 chains. Longest chain 33 peptides. Score 0.599 Taking the results from Round 4 Chains 402, Residues 3020, Estimated correctness of the model 15.8 % 30 chains (430 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 75179 reflections ( 93.20 % complete ) and 13596 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2142 (Rfree = 0.000) for 37247 atoms. Found 167 (238 requested) and removed 169 (119 requested) atoms. Cycle 2: After refmac, R = 0.1999 (Rfree = 0.000) for 37245 atoms. Found 144 (238 requested) and removed 161 (119 requested) atoms. Cycle 3: After refmac, R = 0.1904 (Rfree = 0.000) for 37228 atoms. Found 137 (238 requested) and removed 166 (119 requested) atoms. Cycle 4: After refmac, R = 0.1837 (Rfree = 0.000) for 37199 atoms. Found 129 (238 requested) and removed 149 (119 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1783 (Rfree = 0.000) for 37179 atoms. Found 145 (238 requested) and removed 183 (119 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38597 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 38616 seeds are put forward Round 1: 3036 peptides, 420 chains. Longest chain 36 peptides. Score 0.502 Round 2: 3367 peptides, 385 chains. Longest chain 38 peptides. Score 0.594 Round 3: 3473 peptides, 398 chains. Longest chain 41 peptides. Score 0.602 Round 4: 3421 peptides, 376 chains. Longest chain 43 peptides. Score 0.610 Round 5: 3432 peptides, 362 chains. Longest chain 33 peptides. Score 0.623 Taking the results from Round 5 Chains 378, Residues 3070, Estimated correctness of the model 23.4 % 22 chains (266 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12998 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1972 (Rfree = 0.000) for 37247 atoms. Found 176 (238 requested) and removed 164 (119 requested) atoms. Cycle 7: After refmac, R = 0.1837 (Rfree = 0.000) for 37259 atoms. Found 157 (239 requested) and removed 142 (119 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1792 (Rfree = 0.000) for 37274 atoms. Found 154 (239 requested) and removed 171 (119 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1527 (Rfree = 0.000) for 37257 atoms. Found 34 (239 requested) and removed 136 (119 requested) atoms. Cycle 10: After refmac, R = 0.1474 (Rfree = 0.000) for 37155 atoms. Found 28 (238 requested) and removed 148 (119 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 38451 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 38464 seeds are put forward Round 1: 3117 peptides, 441 chains. Longest chain 29 peptides. Score 0.499 Round 2: 3379 peptides, 377 chains. Longest chain 43 peptides. Score 0.602 Round 3: 3465 peptides, 385 chains. Longest chain 50 peptides. Score 0.610 Round 4: 3450 peptides, 373 chains. Longest chain 41 peptides. Score 0.617 Round 5: 3394 peptides, 380 chains. Longest chain 38 peptides. Score 0.602 Taking the results from Round 4 Chains 399, Residues 3077, Estimated correctness of the model 21.2 % 25 chains (383 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 75179 reflections ( 93.20 % complete ) and 13528 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1924 (Rfree = 0.000) for 37247 atoms. Found 182 (238 requested) and removed 183 (119 requested) atoms. Cycle 12: After refmac, R = 0.1795 (Rfree = 0.000) for 37246 atoms. Found 112 (238 requested) and removed 155 (119 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1755 (Rfree = 0.000) for 37203 atoms. Found 126 (238 requested) and removed 163 (119 requested) atoms. Cycle 14: After refmac, R = 0.1722 (Rfree = 0.000) for 37166 atoms. Found 115 (238 requested) and removed 161 (119 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1698 (Rfree = 0.000) for 37120 atoms. Found 164 (238 requested) and removed 169 (119 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 38478 seeds are put forward NCS extension: 3 residues added (3 deleted due to clashes), 38481 seeds are put forward Round 1: 3078 peptides, 441 chains. Longest chain 32 peptides. Score 0.491 Round 2: 3307 peptides, 385 chains. Longest chain 49 peptides. Score 0.583 Round 3: 3343 peptides, 397 chains. Longest chain 28 peptides. Score 0.580 Round 4: 3351 peptides, 392 chains. Longest chain 32 peptides. Score 0.585 Round 5: 3368 peptides, 393 chains. Longest chain 36 peptides. Score 0.587 Taking the results from Round 5 Chains 415, Residues 2975, Estimated correctness of the model 9.5 % 24 chains (296 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12678 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1918 (Rfree = 0.000) for 37247 atoms. Found 184 (238 requested) and removed 171 (119 requested) atoms. Cycle 17: After refmac, R = 0.1785 (Rfree = 0.000) for 37260 atoms. Found 123 (239 requested) and removed 148 (119 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1751 (Rfree = 0.000) for 37235 atoms. Found 134 (238 requested) and removed 159 (119 requested) atoms. Cycle 19: After refmac, R = 0.1681 (Rfree = 0.000) for 37210 atoms. Found 122 (238 requested) and removed 169 (119 requested) atoms. Cycle 20: After refmac, R = 0.1663 (Rfree = 0.000) for 37163 atoms. Found 101 (238 requested) and removed 178 (119 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38478 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 38487 seeds are put forward Round 1: 2936 peptides, 444 chains. Longest chain 27 peptides. Score 0.458 Round 2: 3198 peptides, 406 chains. Longest chain 41 peptides. Score 0.546 Round 3: 3153 peptides, 396 chains. Longest chain 39 peptides. Score 0.546 Round 4: 3196 peptides, 397 chains. Longest chain 29 peptides. Score 0.553 Round 5: 3258 peptides, 410 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 5 Chains 413, Residues 2848, Estimated correctness of the model 0.0 % 14 chains (165 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11639 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1867 (Rfree = 0.000) for 37247 atoms. Found 169 (238 requested) and removed 158 (119 requested) atoms. Cycle 22: After refmac, R = 0.1788 (Rfree = 0.000) for 37258 atoms. Found 220 (239 requested) and removed 146 (119 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1731 (Rfree = 0.000) for 37332 atoms. Found 184 (239 requested) and removed 165 (119 requested) atoms. Cycle 24: After refmac, R = 0.1445 (Rfree = 0.000) for 37351 atoms. Found 23 (239 requested) and removed 148 (119 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1415 (Rfree = 0.000) for 37226 atoms. Found 28 (238 requested) and removed 131 (119 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38518 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 38531 seeds are put forward Round 1: 2851 peptides, 460 chains. Longest chain 26 peptides. Score 0.425 Round 2: 3100 peptides, 417 chains. Longest chain 27 peptides. Score 0.517 Round 3: 3137 peptides, 420 chains. Longest chain 25 peptides. Score 0.522 Round 4: 3130 peptides, 416 chains. Longest chain 30 peptides. Score 0.524 Round 5: 3142 peptides, 394 chains. Longest chain 41 peptides. Score 0.545 Taking the results from Round 5 Chains 405, Residues 2748, Estimated correctness of the model 0.0 % 21 chains (263 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11649 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1856 (Rfree = 0.000) for 37247 atoms. Found 181 (238 requested) and removed 166 (119 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1761 (Rfree = 0.000) for 37262 atoms. Found 161 (239 requested) and removed 157 (119 requested) atoms. Cycle 28: After refmac, R = 0.1506 (Rfree = 0.000) for 37266 atoms. Found 39 (239 requested) and removed 144 (119 requested) atoms. Cycle 29: After refmac, R = 0.1456 (Rfree = 0.000) for 37161 atoms. Found 22 (238 requested) and removed 126 (119 requested) atoms. Cycle 30: After refmac, R = 0.1444 (Rfree = 0.000) for 37057 atoms. Found 29 (237 requested) and removed 123 (118 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38312 seeds are put forward NCS extension: 48 residues added (22 deleted due to clashes), 38360 seeds are put forward Round 1: 2764 peptides, 460 chains. Longest chain 22 peptides. Score 0.405 Round 2: 3024 peptides, 416 chains. Longest chain 23 peptides. Score 0.503 Round 3: 3031 peptides, 407 chains. Longest chain 33 peptides. Score 0.512 Round 4: 3053 peptides, 411 chains. Longest chain 24 peptides. Score 0.513 Round 5: 3066 peptides, 389 chains. Longest chain 31 peptides. Score 0.535 Taking the results from Round 5 Chains 408, Residues 2677, Estimated correctness of the model 0.0 % 22 chains (276 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 75179 reflections ( 93.20 % complete ) and 11419 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1884 (Rfree = 0.000) for 37247 atoms. Found 223 (238 requested) and removed 168 (119 requested) atoms. Cycle 32: After refmac, R = 0.1789 (Rfree = 0.000) for 37302 atoms. Found 181 (239 requested) and removed 155 (119 requested) atoms. Cycle 33: After refmac, R = 0.1701 (Rfree = 0.000) for 37328 atoms. Found 148 (239 requested) and removed 172 (119 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 37304 atoms. Found 182 (239 requested) and removed 170 (119 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 37316 atoms. Found 150 (239 requested) and removed 161 (119 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.98 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: 2691 peptides, 453 chains. Longest chain 19 peptides. Score 0.395 Round 2: 2968 peptides, 412 chains. Longest chain 29 peptides. Score 0.495 Round 3: 2998 peptides, 413 chains. Longest chain 22 peptides. Score 0.500 Round 4: 2984 peptides, 403 chains. Longest chain 25 peptides. Score 0.506 Round 5: 2980 peptides, 393 chains. Longest chain 31 peptides. Score 0.515 Taking the results from Round 5 Chains 402, Residues 2587, Estimated correctness of the model 0.0 % 16 chains (212 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10797 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1824 (Rfree = 0.000) for 37247 atoms. Found 176 (238 requested) and removed 155 (119 requested) atoms. Cycle 37: After refmac, R = 0.1751 (Rfree = 0.000) for 37268 atoms. Found 173 (239 requested) and removed 160 (119 requested) atoms. Cycle 38: After refmac, R = 0.1682 (Rfree = 0.000) for 37281 atoms. Found 151 (239 requested) and removed 142 (119 requested) atoms. Cycle 39: After refmac, R = 0.1656 (Rfree = 0.000) for 37290 atoms. Found 150 (239 requested) and removed 172 (119 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1610 (Rfree = 0.000) for 37268 atoms. Found 147 (239 requested) and removed 166 (119 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38549 seeds are put forward NCS extension: 0 residues added, 38549 seeds are put forward Round 1: 2568 peptides, 447 chains. Longest chain 18 peptides. Score 0.373 Round 2: 2846 peptides, 419 chains. Longest chain 29 peptides. Score 0.463 Round 3: 2890 peptides, 407 chains. Longest chain 24 peptides. Score 0.483 Round 4: 2909 peptides, 393 chains. Longest chain 31 peptides. Score 0.500 Round 5: 2908 peptides, 408 chains. Longest chain 29 peptides. Score 0.486 Taking the results from Round 4 Chains 403, Residues 2516, Estimated correctness of the model 0.0 % 14 chains (135 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10133 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1826 (Rfree = 0.000) for 37247 atoms. Found 185 (238 requested) and removed 154 (119 requested) atoms. Cycle 42: After refmac, R = 0.1756 (Rfree = 0.000) for 37278 atoms. Found 224 (239 requested) and removed 164 (119 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1507 (Rfree = 0.000) for 37338 atoms. Found 31 (239 requested) and removed 154 (119 requested) atoms. Cycle 44: After refmac, R = 0.1458 (Rfree = 0.000) for 37215 atoms. Found 23 (238 requested) and removed 131 (119 requested) atoms. Cycle 45: After refmac, R = 0.1451 (Rfree = 0.000) for 37107 atoms. Found 20 (238 requested) and removed 124 (119 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38197 seeds are put forward NCS extension: 0 residues added, 38197 seeds are put forward Round 1: 2553 peptides, 455 chains. Longest chain 19 peptides. Score 0.361 Round 2: 2814 peptides, 400 chains. Longest chain 26 peptides. Score 0.474 Round 3: 2891 peptides, 398 chains. Longest chain 24 peptides. Score 0.492 Round 4: 2914 peptides, 411 chains. Longest chain 24 peptides. Score 0.485 Round 5: 2914 peptides, 396 chains. Longest chain 23 peptides. Score 0.499 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 402, Residues 2518, Estimated correctness of the model 0.0 % 14 chains (134 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 402 chains (2518 residues) following loop building 14 chains (134 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75179 reflections ( 93.20 % complete ) and 10161 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1793 (Rfree = 0.000) for 37247 atoms. Found 0 (238 requested) and removed 119 (119 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1759 (Rfree = 0.000) for 37128 atoms. Found 0 (238 requested) and removed 119 (119 requested) atoms. Cycle 48: After refmac, R = 0.1709 (Rfree = 0.000) for 37009 atoms. Found 0 (237 requested) and removed 118 (118 requested) atoms. Cycle 49: After refmac, R = 0.1645 (Rfree = 0.000) for 36891 atoms. TimeTaking 448.32