Mon 24 Dec 07:54:11 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-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-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-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-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 07:54:16 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-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-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 4422 and 0 Target number of residues in the AU: 4422 Target solvent content: 0.6614 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-4.0-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-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 1.00 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 4.000 Wilson plot Bfac: 85.98 Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 0 restraints for refining 45368 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3243 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2947 (Rfree = 0.000) for 45368 atoms. Found 215 (215 requested) and removed 185 (107 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.27 Search for helices and strands: 0 residues in 0 chains, 46290 seeds are put forward NCS extension: 0 residues added, 46290 seeds are put forward Round 1: 2039 peptides, 394 chains. Longest chain 14 peptides. Score 0.298 Round 2: 2603 peptides, 394 chains. Longest chain 21 peptides. Score 0.434 Round 3: 2747 peptides, 376 chains. Longest chain 26 peptides. Score 0.483 Round 4: 2746 peptides, 366 chains. Longest chain 21 peptides. Score 0.492 Round 5: 2820 peptides, 371 chains. Longest chain 23 peptides. Score 0.503 Taking the results from Round 5 Chains 375, Residues 2449, Estimated correctness of the model 0.0 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9626 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2296 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 136 (88 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2097 (Rfree = 0.000) for 37146 atoms. Found 176 (176 requested) and removed 129 (88 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1977 (Rfree = 0.000) for 37193 atoms. Found 176 (176 requested) and removed 149 (88 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2003 (Rfree = 0.000) for 37220 atoms. Found 176 (176 requested) and removed 161 (88 requested) atoms. Cycle 5: After refmac, R = 0.1950 (Rfree = 0.000) for 37235 atoms. Found 176 (176 requested) and removed 153 (88 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.20 Search for helices and strands: 0 residues in 0 chains, 38660 seeds are put forward NCS extension: 0 residues added, 38660 seeds are put forward Round 1: 2298 peptides, 397 chains. Longest chain 21 peptides. Score 0.360 Round 2: 2803 peptides, 395 chains. Longest chain 22 peptides. Score 0.477 Round 3: 2853 peptides, 395 chains. Longest chain 21 peptides. Score 0.487 Round 4: 2857 peptides, 363 chains. Longest chain 26 peptides. Score 0.517 Round 5: 2877 peptides, 366 chains. Longest chain 28 peptides. Score 0.519 Taking the results from Round 5 Chains 371, Residues 2511, Estimated correctness of the model 0.0 % 9 chains (104 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 10052 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2012 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 166 (88 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 7: After refmac, R = 0.1926 (Rfree = 0.000) for 37116 atoms. Found 176 (176 requested) and removed 164 (88 requested) atoms. Cycle 8: After refmac, R = 0.1392 (Rfree = 0.000) for 37128 atoms. Found 32 (176 requested) and removed 132 (88 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1293 (Rfree = 0.000) for 37028 atoms. Found 31 (175 requested) and removed 130 (87 requested) atoms. Cycle 10: After refmac, R = 0.1247 (Rfree = 0.000) for 36929 atoms. Found 21 (175 requested) and removed 120 (87 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38197 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 38221 seeds are put forward Round 1: 2453 peptides, 415 chains. Longest chain 19 peptides. Score 0.378 Round 2: 2779 peptides, 395 chains. Longest chain 22 peptides. Score 0.471 Round 3: 2796 peptides, 379 chains. Longest chain 22 peptides. Score 0.490 Round 4: 2831 peptides, 371 chains. Longest chain 27 peptides. Score 0.505 Round 5: 2828 peptides, 371 chains. Longest chain 26 peptides. Score 0.504 Taking the results from Round 4 Chains 374, Residues 2460, Estimated correctness of the model 0.0 % 10 chains (110 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9943 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1924 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 176 (88 requested) atoms. Cycle 12: After refmac, R = 0.1835 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 154 (88 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1804 (Rfree = 0.000) for 37128 atoms. Found 176 (176 requested) and removed 174 (88 requested) atoms. Cycle 14: After refmac, R = 0.1728 (Rfree = 0.000) for 37130 atoms. Found 176 (176 requested) and removed 166 (88 requested) atoms. Cycle 15: After refmac, R = 0.1223 (Rfree = 0.000) for 37140 atoms. Found 28 (176 requested) and removed 125 (88 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38311 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 38327 seeds are put forward Round 1: 2345 peptides, 416 chains. Longest chain 15 peptides. Score 0.351 Round 2: 2698 peptides, 389 chains. Longest chain 31 peptides. Score 0.460 Round 3: 2749 peptides, 391 chains. Longest chain 39 peptides. Score 0.469 Round 4: 2837 peptides, 388 chains. Longest chain 25 peptides. Score 0.490 Round 5: 2819 peptides, 390 chains. Longest chain 39 peptides. Score 0.485 Taking the results from Round 4 Chains 394, Residues 2449, Estimated correctness of the model 0.0 % 13 chains (142 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 10007 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1862 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 170 (88 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1767 (Rfree = 0.000) for 37112 atoms. Found 176 (176 requested) and removed 148 (88 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1287 (Rfree = 0.000) for 37140 atoms. Found 19 (176 requested) and removed 123 (88 requested) atoms. Cycle 19: After refmac, R = 0.1190 (Rfree = 0.000) for 37036 atoms. Found 20 (175 requested) and removed 130 (87 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1145 (Rfree = 0.000) for 36926 atoms. Found 19 (175 requested) and removed 112 (87 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.24 Search for helices and strands: 0 residues in 0 chains, 38067 seeds are put forward NCS extension: 0 residues added, 38067 seeds are put forward Round 1: 2327 peptides, 418 chains. Longest chain 16 peptides. Score 0.345 Round 2: 2663 peptides, 407 chains. Longest chain 21 peptides. Score 0.435 Round 3: 2668 peptides, 400 chains. Longest chain 19 peptides. Score 0.443 Round 4: 2747 peptides, 389 chains. Longest chain 21 peptides. Score 0.470 Round 5: 2708 peptides, 375 chains. Longest chain 31 peptides. Score 0.476 Taking the results from Round 5 Chains 381, Residues 2333, Estimated correctness of the model 0.0 % 10 chains (86 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9307 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1892 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 152 (88 requested) atoms. Cycle 22: After refmac, R = 0.1847 (Rfree = 0.000) for 37130 atoms. Found 176 (176 requested) and removed 139 (88 requested) atoms. Cycle 23: After refmac, R = 0.1803 (Rfree = 0.000) for 37167 atoms. Found 176 (176 requested) and removed 171 (88 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1713 (Rfree = 0.000) for 37172 atoms. Found 176 (176 requested) and removed 158 (88 requested) atoms. Cycle 25: After refmac, R = 0.1143 (Rfree = 0.000) for 37190 atoms. Found 26 (176 requested) and removed 120 (88 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38382 seeds are put forward NCS extension: 0 residues added, 38382 seeds are put forward Round 1: 2114 peptides, 388 chains. Longest chain 16 peptides. Score 0.324 Round 2: 2564 peptides, 396 chains. Longest chain 20 peptides. Score 0.423 Round 3: 2604 peptides, 386 chains. Longest chain 22 peptides. Score 0.442 Round 4: 2577 peptides, 383 chains. Longest chain 20 peptides. Score 0.439 Round 5: 2645 peptides, 393 chains. Longest chain 20 peptides. Score 0.444 Taking the results from Round 5 Chains 394, Residues 2252, Estimated correctness of the model 0.0 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 8823 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1861 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 158 (88 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1800 (Rfree = 0.000) for 37124 atoms. Found 176 (176 requested) and removed 132 (88 requested) atoms. Cycle 28: After refmac, R = 0.1258 (Rfree = 0.000) for 37168 atoms. Found 30 (176 requested) and removed 123 (88 requested) atoms. Cycle 29: After refmac, R = 0.1168 (Rfree = 0.000) for 37075 atoms. Found 23 (176 requested) and removed 124 (88 requested) atoms. Cycle 30: After refmac, R = 0.1116 (Rfree = 0.000) for 36974 atoms. Found 20 (175 requested) and removed 110 (87 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38121 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 38143 seeds are put forward Round 1: 2173 peptides, 406 chains. Longest chain 18 peptides. Score 0.319 Round 2: 2435 peptides, 403 chains. Longest chain 21 peptides. Score 0.387 Round 3: 2516 peptides, 385 chains. Longest chain 30 peptides. Score 0.424 Round 4: 2525 peptides, 377 chains. Longest chain 22 peptides. Score 0.434 Round 5: 2564 peptides, 389 chains. Longest chain 19 peptides. Score 0.430 Taking the results from Round 4 Chains 386, Residues 2148, Estimated correctness of the model 0.0 % 11 chains (117 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8668 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1845 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 195 (88 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1766 (Rfree = 0.000) for 37087 atoms. Found 176 (176 requested) and removed 159 (88 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1722 (Rfree = 0.000) for 37104 atoms. Found 176 (176 requested) and removed 175 (88 requested) atoms. Cycle 34: After refmac, R = 0.1209 (Rfree = 0.000) for 37105 atoms. Found 28 (176 requested) and removed 128 (88 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1122 (Rfree = 0.000) for 37005 atoms. Found 23 (175 requested) and removed 126 (87 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38092 seeds are put forward NCS extension: 0 residues added, 38092 seeds are put forward Round 1: 2033 peptides, 387 chains. Longest chain 15 peptides. Score 0.304 Round 2: 2334 peptides, 381 chains. Longest chain 18 peptides. Score 0.386 Round 3: 2424 peptides, 387 chains. Longest chain 19 peptides. Score 0.401 Round 4: 2454 peptides, 385 chains. Longest chain 22 peptides. Score 0.409 Round 5: 2410 peptides, 378 chains. Longest chain 23 peptides. Score 0.407 Taking the results from Round 4 Chains 389, Residues 2069, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 8115 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1804 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 156 (88 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1727 (Rfree = 0.000) for 37126 atoms. Found 176 (176 requested) and removed 145 (88 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1226 (Rfree = 0.000) for 37157 atoms. Found 44 (176 requested) and removed 124 (88 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1123 (Rfree = 0.000) for 37077 atoms. Found 28 (176 requested) and removed 121 (88 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1073 (Rfree = 0.000) for 36984 atoms. Found 21 (175 requested) and removed 112 (87 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38014 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 38021 seeds are put forward Round 1: 1988 peptides, 381 chains. Longest chain 19 peptides. Score 0.299 Round 2: 2359 peptides, 397 chains. Longest chain 20 peptides. Score 0.375 Round 3: 2351 peptides, 373 chains. Longest chain 22 peptides. Score 0.398 Round 4: 2397 peptides, 376 chains. Longest chain 22 peptides. Score 0.406 Round 5: 2394 peptides, 368 chains. Longest chain 25 peptides. Score 0.413 Taking the results from Round 5 Chains 369, Residues 2026, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 7813 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1841 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 122 (88 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 37160 atoms. Found 176 (176 requested) and removed 132 (88 requested) atoms. Cycle 43: After refmac, R = 0.1745 (Rfree = 0.000) for 37204 atoms. Found 176 (176 requested) and removed 156 (88 requested) atoms. Cycle 44: After refmac, R = 0.1745 (Rfree = 0.000) for 37224 atoms. Found 176 (176 requested) and removed 171 (88 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1716 (Rfree = 0.000) for 37229 atoms. Found 176 (176 requested) and removed 141 (88 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.24 Search for helices and strands: 0 residues in 0 chains, 38392 seeds are put forward NCS extension: 0 residues added, 38392 seeds are put forward Round 1: 1744 peptides, 346 chains. Longest chain 13 peptides. Score 0.274 Round 2: 2064 peptides, 355 chains. Longest chain 17 peptides. Score 0.348 Round 3: 2220 peptides, 367 chains. Longest chain 18 peptides. Score 0.373 Round 4: 2223 peptides, 353 chains. Longest chain 20 peptides. Score 0.389 Round 5: 2244 peptides, 356 chains. Longest chain 21 peptides. Score 0.391 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 357, Residues 1888, Estimated correctness of the model 0.0 % 7 chains (58 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2pnk-4_warpNtrace.pdb as input Building loops using Loopy2018 357 chains (1888 residues) following loop building 7 chains (58 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 54586 reflections ( 92.59 % complete ) and 7406 restraints for refining 37105 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1817 (Rfree = 0.000) for 37105 atoms. Found 0 (176 requested) and removed 88 (88 requested) atoms. Cycle 47: After refmac, R = 0.1773 (Rfree = 0.000) for 37017 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Cycle 48: After refmac, R = 0.1728 (Rfree = 0.000) for 36930 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Cycle 49: After refmac, R = 0.1706 (Rfree = 0.000) for 36843 atoms. TimeTaking 362.43