Mon 24 Dec 07:45:09 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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 07:45:13 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.4-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 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-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-3.4-parrot-noncs.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 45592 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3028 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2411 (Rfree = 0.000) for 45592 atoms. Found 344 (344 requested) and removed 234 (172 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 46749 seeds are put forward NCS extension: 0 residues added, 46749 seeds are put forward Round 1: 2965 peptides, 490 chains. Longest chain 19 peptides. Score 0.421 Round 2: 3388 peptides, 445 chains. Longest chain 23 peptides. Score 0.548 Round 3: 3558 peptides, 426 chains. Longest chain 39 peptides. Score 0.594 Round 4: 3600 peptides, 404 chains. Longest chain 37 peptides. Score 0.618 Round 5: 3605 peptides, 390 chains. Longest chain 40 peptides. Score 0.630 Taking the results from Round 5 Chains 404, Residues 3215, Estimated correctness of the model 38.2 % 25 chains (377 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14078 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2130 (Rfree = 0.000) for 37359 atoms. Found 218 (282 requested) and removed 197 (141 requested) atoms. Cycle 2: After refmac, R = 0.1955 (Rfree = 0.000) for 37380 atoms. Found 112 (282 requested) and removed 167 (141 requested) atoms. Cycle 3: After refmac, R = 0.1888 (Rfree = 0.000) for 37325 atoms. Found 99 (281 requested) and removed 168 (140 requested) atoms. Cycle 4: After refmac, R = 0.1823 (Rfree = 0.000) for 37256 atoms. Found 90 (281 requested) and removed 179 (140 requested) atoms. Cycle 5: After refmac, R = 0.1776 (Rfree = 0.000) for 37167 atoms. Found 90 (280 requested) and removed 171 (140 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38449 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 38471 seeds are put forward Round 1: 3339 peptides, 440 chains. Longest chain 31 peptides. Score 0.543 Round 2: 3653 peptides, 404 chains. Longest chain 33 peptides. Score 0.627 Round 3: 3663 peptides, 389 chains. Longest chain 32 peptides. Score 0.640 Round 4: 3620 peptides, 379 chains. Longest chain 36 peptides. Score 0.640 Round 5: 3592 peptides, 380 chains. Longest chain 35 peptides. Score 0.635 Taking the results from Round 4 Chains 400, Residues 3241, Estimated correctness of the model 41.2 % 27 chains (425 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14306 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1963 (Rfree = 0.000) for 37359 atoms. Found 183 (282 requested) and removed 203 (141 requested) atoms. Cycle 7: After refmac, R = 0.1819 (Rfree = 0.000) for 37339 atoms. Found 71 (281 requested) and removed 162 (140 requested) atoms. Cycle 8: After refmac, R = 0.1786 (Rfree = 0.000) for 37248 atoms. Found 85 (281 requested) and removed 146 (140 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1754 (Rfree = 0.000) for 37187 atoms. Found 100 (280 requested) and removed 148 (140 requested) atoms. Cycle 10: After refmac, R = 0.1604 (Rfree = 0.000) for 37139 atoms. Found 32 (280 requested) and removed 150 (140 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38269 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 38279 seeds are put forward Round 1: 3299 peptides, 427 chains. Longest chain 33 peptides. Score 0.547 Round 2: 3568 peptides, 388 chains. Longest chain 37 peptides. Score 0.625 Round 3: 3573 peptides, 380 chains. Longest chain 43 peptides. Score 0.632 Round 4: 3587 peptides, 394 chains. Longest chain 35 peptides. Score 0.624 Round 5: 3569 peptides, 392 chains. Longest chain 33 peptides. Score 0.622 Taking the results from Round 3 Chains 411, Residues 3193, Estimated correctness of the model 38.8 % 31 chains (473 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14433 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1910 (Rfree = 0.000) for 37359 atoms. Found 246 (282 requested) and removed 202 (141 requested) atoms. Cycle 12: After refmac, R = 0.1757 (Rfree = 0.000) for 37403 atoms. Found 93 (282 requested) and removed 159 (141 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1651 (Rfree = 0.000) for 37337 atoms. Found 48 (281 requested) and removed 148 (140 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1642 (Rfree = 0.000) for 37237 atoms. Found 27 (281 requested) and removed 142 (140 requested) atoms. Cycle 15: After refmac, R = 0.1594 (Rfree = 0.000) for 37122 atoms. Found 29 (280 requested) and removed 140 (140 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38236 seeds are put forward NCS extension: 0 residues added, 38236 seeds are put forward Round 1: 3249 peptides, 433 chains. Longest chain 25 peptides. Score 0.532 Round 2: 3498 peptides, 398 chains. Longest chain 54 peptides. Score 0.606 Round 3: 3500 peptides, 397 chains. Longest chain 32 peptides. Score 0.607 Round 4: 3509 peptides, 377 chains. Longest chain 59 peptides. Score 0.624 Round 5: 3493 peptides, 397 chains. Longest chain 47 peptides. Score 0.606 Taking the results from Round 4 Chains 403, Residues 3132, Estimated correctness of the model 36.3 % 36 chains (627 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 14907 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1979 (Rfree = 0.000) for 37359 atoms. Found 200 (282 requested) and removed 231 (141 requested) atoms. Cycle 17: After refmac, R = 0.1827 (Rfree = 0.000) for 37328 atoms. Found 97 (281 requested) and removed 153 (140 requested) atoms. Cycle 18: After refmac, R = 0.1783 (Rfree = 0.000) for 37272 atoms. Found 115 (281 requested) and removed 143 (140 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1743 (Rfree = 0.000) for 37244 atoms. Found 69 (281 requested) and removed 147 (140 requested) atoms. Cycle 20: After refmac, R = 0.1696 (Rfree = 0.000) for 37166 atoms. Found 84 (280 requested) and removed 145 (140 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38345 seeds are put forward NCS extension: 0 residues added, 38345 seeds are put forward Round 1: 3254 peptides, 436 chains. Longest chain 34 peptides. Score 0.530 Round 2: 3462 peptides, 409 chains. Longest chain 30 peptides. Score 0.591 Round 3: 3490 peptides, 394 chains. Longest chain 40 peptides. Score 0.608 Round 4: 3554 peptides, 402 chains. Longest chain 38 peptides. Score 0.612 Round 5: 3539 peptides, 400 chains. Longest chain 48 peptides. Score 0.611 Taking the results from Round 4 Chains 419, Residues 3152, Estimated correctness of the model 32.5 % 34 chains (563 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 14681 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1986 (Rfree = 0.000) for 37359 atoms. Found 241 (282 requested) and removed 205 (141 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1817 (Rfree = 0.000) for 37395 atoms. Found 62 (282 requested) and removed 150 (141 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1803 (Rfree = 0.000) for 37307 atoms. Found 96 (281 requested) and removed 146 (140 requested) atoms. Cycle 24: After refmac, R = 0.1791 (Rfree = 0.000) for 37257 atoms. Found 85 (281 requested) and removed 148 (140 requested) atoms. Cycle 25: After refmac, R = 0.1792 (Rfree = 0.000) for 37194 atoms. Found 87 (280 requested) and removed 145 (140 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38413 seeds are put forward NCS extension: 20 residues added (12 deleted due to clashes), 38433 seeds are put forward Round 1: 3127 peptides, 448 chains. Longest chain 25 peptides. Score 0.495 Round 2: 3339 peptides, 408 chains. Longest chain 37 peptides. Score 0.570 Round 3: 3354 peptides, 398 chains. Longest chain 34 peptides. Score 0.581 Round 4: 3362 peptides, 388 chains. Longest chain 38 peptides. Score 0.590 Round 5: 3349 peptides, 410 chains. Longest chain 48 peptides. Score 0.570 Taking the results from Round 4 Chains 402, Residues 2974, Estimated correctness of the model 25.4 % 26 chains (398 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 13294 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1961 (Rfree = 0.000) for 37359 atoms. Found 192 (282 requested) and removed 187 (141 requested) atoms. Cycle 27: After refmac, R = 0.1829 (Rfree = 0.000) for 37364 atoms. Found 80 (282 requested) and removed 151 (141 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1787 (Rfree = 0.000) for 37293 atoms. Found 116 (281 requested) and removed 146 (140 requested) atoms. Cycle 29: After refmac, R = 0.1762 (Rfree = 0.000) for 37263 atoms. Found 79 (281 requested) and removed 144 (140 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1719 (Rfree = 0.000) for 37198 atoms. Found 69 (280 requested) and removed 146 (140 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 2.86 Search for helices and strands: 0 residues in 0 chains, 38392 seeds are put forward NCS extension: 8 residues added (7 deleted due to clashes), 38400 seeds are put forward Round 1: 2916 peptides, 447 chains. Longest chain 21 peptides. Score 0.451 Round 2: 3250 peptides, 417 chains. Longest chain 32 peptides. Score 0.546 Round 3: 3292 peptides, 418 chains. Longest chain 28 peptides. Score 0.553 Round 4: 3248 peptides, 408 chains. Longest chain 37 peptides. Score 0.553 Round 5: 3270 peptides, 412 chains. Longest chain 40 peptides. Score 0.554 Taking the results from Round 5 Chains 422, Residues 2858, Estimated correctness of the model 13.0 % 18 chains (200 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 11859 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1923 (Rfree = 0.000) for 37359 atoms. Found 194 (282 requested) and removed 174 (141 requested) atoms. Cycle 32: After refmac, R = 0.1803 (Rfree = 0.000) for 37379 atoms. Found 104 (282 requested) and removed 151 (141 requested) atoms. Cycle 33: After refmac, R = 0.1741 (Rfree = 0.000) for 37332 atoms. Found 119 (281 requested) and removed 145 (140 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1720 (Rfree = 0.000) for 37306 atoms. Found 120 (281 requested) and removed 152 (140 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1676 (Rfree = 0.000) for 37274 atoms. Found 147 (281 requested) and removed 145 (140 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 38447 seeds are put forward NCS extension: 0 residues added, 38447 seeds are put forward Round 1: 2752 peptides, 454 chains. Longest chain 21 peptides. Score 0.408 Round 2: 3105 peptides, 418 chains. Longest chain 38 peptides. Score 0.517 Round 3: 3140 peptides, 428 chains. Longest chain 25 peptides. Score 0.515 Round 4: 3124 peptides, 412 chains. Longest chain 33 peptides. Score 0.526 Round 5: 3091 peptides, 397 chains. Longest chain 33 peptides. Score 0.533 Taking the results from Round 5 Chains 410, Residues 2694, Estimated correctness of the model 5.3 % 20 chains (253 residues) have been docked in sequence ------------------------------------------------------ 89442 reflections ( 93.49 % complete ) and 11447 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1882 (Rfree = 0.000) for 37359 atoms. Found 202 (282 requested) and removed 177 (141 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1785 (Rfree = 0.000) for 37384 atoms. Found 121 (282 requested) and removed 150 (141 requested) atoms. Cycle 38: After refmac, R = 0.1743 (Rfree = 0.000) for 37355 atoms. Found 171 (282 requested) and removed 145 (141 requested) atoms. Cycle 39: After refmac, R = 0.1704 (Rfree = 0.000) for 37381 atoms. Found 126 (282 requested) and removed 150 (141 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1658 (Rfree = 0.000) for 37357 atoms. Found 124 (282 requested) and removed 149 (141 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38590 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 38598 seeds are put forward Round 1: 2613 peptides, 438 chains. Longest chain 21 peptides. Score 0.392 Round 2: 2964 peptides, 426 chains. Longest chain 23 peptides. Score 0.481 Round 3: 2978 peptides, 423 chains. Longest chain 25 peptides. Score 0.487 Round 4: 3072 peptides, 410 chains. Longest chain 35 peptides. Score 0.518 Round 5: 3083 peptides, 420 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 4 Chains 418, Residues 2662, Estimated correctness of the model 0.0 % 19 chains (221 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 11146 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1826 (Rfree = 0.000) for 37359 atoms. Found 189 (282 requested) and removed 168 (141 requested) atoms. Cycle 42: After refmac, R = 0.1732 (Rfree = 0.000) for 37380 atoms. Found 105 (282 requested) and removed 151 (141 requested) atoms. Cycle 43: After refmac, R = 0.1707 (Rfree = 0.000) for 37334 atoms. Found 113 (281 requested) and removed 145 (140 requested) atoms. Cycle 44: After refmac, R = 0.1668 (Rfree = 0.000) for 37302 atoms. Found 113 (281 requested) and removed 152 (140 requested) atoms. Cycle 45: After refmac, R = 0.1507 (Rfree = 0.000) for 37263 atoms. Found 31 (281 requested) and removed 145 (140 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 38368 seeds are put forward NCS extension: 0 residues added, 38368 seeds are put forward Round 1: 2639 peptides, 435 chains. Longest chain 20 peptides. Score 0.401 Round 2: 2961 peptides, 420 chains. Longest chain 22 peptides. Score 0.486 Round 3: 2983 peptides, 409 chains. Longest chain 30 peptides. Score 0.501 Round 4: 2980 peptides, 401 chains. Longest chain 30 peptides. Score 0.507 Round 5: 2930 peptides, 392 chains. Longest chain 28 peptides. Score 0.506 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 405, Residues 2579, Estimated correctness of the model 0.0 % 11 chains (130 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 405 chains (2579 residues) following loop building 11 chains (130 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 89442 reflections ( 93.49 % complete ) and 10423 restraints for refining 37359 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1795 (Rfree = 0.000) for 37359 atoms. Found 0 (282 requested) and removed 74 (141 requested) atoms. Cycle 47: After refmac, R = 0.1773 (Rfree = 0.000) for 37285 atoms. Found 0 (281 requested) and removed 70 (140 requested) atoms. Cycle 48: After refmac, R = 0.1752 (Rfree = 0.000) for 37215 atoms. Found 0 (280 requested) and removed 104 (140 requested) atoms. Cycle 49: After refmac, R = 0.1760 (Rfree = 0.000) for 37111 atoms. Found 0 (280 requested) and removed 140 (140 requested) atoms. Writing output files ... TimeTaking 373.53