null Mon 24 Dec 07:30:54 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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 07:30:59 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-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 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-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-3.6-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 3.600 Wilson plot Bfac: 75.44 75179 reflections ( 93.20 % complete ) and 0 restraints for refining 45651 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3118 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2663 (Rfree = 0.000) for 45651 atoms. Found 292 (292 requested) and removed 238 (146 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 46754 seeds are put forward NCS extension: 0 residues added, 46754 seeds are put forward Round 1: 2701 peptides, 479 chains. Longest chain 16 peptides. Score 0.371 Round 2: 3165 peptides, 435 chains. Longest chain 23 peptides. Score 0.514 Round 3: 3290 peptides, 405 chains. Longest chain 41 peptides. Score 0.564 Round 4: 3363 peptides, 394 chains. Longest chain 34 peptides. Score 0.586 Round 5: 3357 peptides, 385 chains. Longest chain 32 peptides. Score 0.592 Taking the results from Round 5 Chains 401, Residues 2972, Estimated correctness of the model 11.5 % 19 chains (293 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12730 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2129 (Rfree = 0.000) for 37247 atoms. Found 204 (238 requested) and removed 193 (119 requested) atoms. Cycle 2: After refmac, R = 0.1972 (Rfree = 0.000) for 37258 atoms. Found 168 (239 requested) and removed 183 (119 requested) atoms. Cycle 3: After refmac, R = 0.1855 (Rfree = 0.000) for 37243 atoms. Found 166 (238 requested) and removed 195 (119 requested) atoms. Cycle 4: After refmac, R = 0.1764 (Rfree = 0.000) for 37214 atoms. Found 150 (238 requested) and removed 190 (119 requested) atoms. Cycle 5: After refmac, R = 0.1690 (Rfree = 0.000) for 37174 atoms. Found 138 (238 requested) and removed 195 (119 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 38530 seeds are put forward NCS extension: 0 residues added, 38530 seeds are put forward Round 1: 3166 peptides, 452 chains. Longest chain 24 peptides. Score 0.499 Round 2: 3346 peptides, 411 chains. Longest chain 35 peptides. Score 0.569 Round 3: 3363 peptides, 389 chains. Longest chain 32 peptides. Score 0.590 Round 4: 3391 peptides, 384 chains. Longest chain 39 peptides. Score 0.599 Round 5: 3397 peptides, 394 chains. Longest chain 33 peptides. Score 0.592 Taking the results from Round 4 Chains 407, Residues 3007, Estimated correctness of the model 14.3 % 23 chains (365 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 13184 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1950 (Rfree = 0.000) for 37247 atoms. Found 205 (238 requested) and removed 182 (119 requested) atoms. Cycle 7: After refmac, R = 0.1830 (Rfree = 0.000) for 37270 atoms. Found 205 (239 requested) and removed 176 (119 requested) atoms. Cycle 8: After refmac, R = 0.1750 (Rfree = 0.000) for 37299 atoms. Found 199 (239 requested) and removed 172 (119 requested) atoms. Cycle 9: After refmac, R = 0.1703 (Rfree = 0.000) for 37326 atoms. Found 132 (239 requested) and removed 178 (119 requested) atoms. Cycle 10: After refmac, R = 0.1455 (Rfree = 0.000) for 37280 atoms. Found 42 (239 requested) and removed 157 (119 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38530 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 38554 seeds are put forward Round 1: 3095 peptides, 433 chains. Longest chain 32 peptides. Score 0.502 Round 2: 3333 peptides, 404 chains. Longest chain 29 peptides. Score 0.572 Round 3: 3280 peptides, 383 chains. Longest chain 41 peptides. Score 0.580 Round 4: 3309 peptides, 382 chains. Longest chain 36 peptides. Score 0.586 Round 5: 3343 peptides, 380 chains. Longest chain 34 peptides. Score 0.594 Taking the results from Round 5 Chains 400, Residues 2963, Estimated correctness of the model 12.3 % 22 chains (315 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12770 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1944 (Rfree = 0.000) for 37247 atoms. Found 179 (238 requested) and removed 166 (119 requested) atoms. Cycle 12: After refmac, R = 0.1809 (Rfree = 0.000) for 37260 atoms. Found 154 (239 requested) and removed 155 (119 requested) atoms. Cycle 13: After refmac, R = 0.1550 (Rfree = 0.000) for 37259 atoms. Found 33 (239 requested) and removed 156 (119 requested) atoms. Cycle 14: After refmac, R = 0.1476 (Rfree = 0.000) for 37136 atoms. Found 39 (238 requested) and removed 134 (119 requested) atoms. Cycle 15: After refmac, R = 0.1442 (Rfree = 0.000) for 37041 atoms. Found 23 (237 requested) and removed 122 (118 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38307 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 38312 seeds are put forward Round 1: 3069 peptides, 436 chains. Longest chain 42 peptides. Score 0.494 Round 2: 3263 peptides, 400 chains. Longest chain 34 peptides. Score 0.563 Round 3: 3242 peptides, 392 chains. Longest chain 32 peptides. Score 0.566 Round 4: 3238 peptides, 379 chains. Longest chain 30 peptides. Score 0.576 Round 5: 3186 peptides, 369 chains. Longest chain 33 peptides. Score 0.575 Taking the results from Round 4 Chains 395, Residues 2859, Estimated correctness of the model 5.1 % 18 chains (208 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11834 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1900 (Rfree = 0.000) for 37247 atoms. Found 176 (238 requested) and removed 163 (119 requested) atoms. Cycle 17: After refmac, R = 0.1796 (Rfree = 0.000) for 37260 atoms. Found 168 (239 requested) and removed 150 (119 requested) atoms. Cycle 18: After refmac, R = 0.1711 (Rfree = 0.000) for 37278 atoms. Found 133 (239 requested) and removed 151 (119 requested) atoms. Cycle 19: After refmac, R = 0.1646 (Rfree = 0.000) for 37260 atoms. Found 105 (239 requested) and removed 156 (119 requested) atoms. Cycle 20: After refmac, R = 0.1611 (Rfree = 0.000) for 37209 atoms. Found 126 (238 requested) and removed 166 (119 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38578 seeds are put forward NCS extension: 0 residues added, 38578 seeds are put forward Round 1: 2899 peptides, 438 chains. Longest chain 28 peptides. Score 0.456 Round 2: 3241 peptides, 403 chains. Longest chain 32 peptides. Score 0.556 Round 3: 3199 peptides, 410 chains. Longest chain 29 peptides. Score 0.542 Round 4: 3231 peptides, 388 chains. Longest chain 32 peptides. Score 0.567 Round 5: 3206 peptides, 394 chains. Longest chain 31 peptides. Score 0.557 Taking the results from Round 4 Chains 405, Residues 2843, Estimated correctness of the model 1.3 % 15 chains (193 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11790 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1825 (Rfree = 0.000) for 37247 atoms. Found 166 (238 requested) and removed 157 (119 requested) atoms. Cycle 22: After refmac, R = 0.1720 (Rfree = 0.000) for 37256 atoms. Found 180 (239 requested) and removed 157 (119 requested) atoms. Cycle 23: After refmac, R = 0.1655 (Rfree = 0.000) for 37279 atoms. Found 146 (239 requested) and removed 145 (119 requested) atoms. Cycle 24: After refmac, R = 0.1587 (Rfree = 0.000) for 37280 atoms. Found 143 (239 requested) and removed 155 (119 requested) atoms. Cycle 25: After refmac, R = 0.1575 (Rfree = 0.000) for 37268 atoms. Found 150 (239 requested) and removed 156 (119 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38622 seeds are put forward NCS extension: 0 residues added, 38622 seeds are put forward Round 1: 2822 peptides, 443 chains. Longest chain 24 peptides. Score 0.435 Round 2: 3124 peptides, 395 chains. Longest chain 32 peptides. Score 0.541 Round 3: 3161 peptides, 397 chains. Longest chain 38 peptides. Score 0.546 Round 4: 3171 peptides, 406 chains. Longest chain 32 peptides. Score 0.540 Round 5: 3126 peptides, 406 chains. Longest chain 29 peptides. Score 0.532 Taking the results from Round 3 Chains 408, Residues 2764, Estimated correctness of the model 0.0 % 13 chains (179 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11378 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1778 (Rfree = 0.000) for 37247 atoms. Found 188 (238 requested) and removed 160 (119 requested) atoms. Cycle 27: After refmac, R = 0.1668 (Rfree = 0.000) for 37275 atoms. Found 147 (239 requested) and removed 142 (119 requested) atoms. Cycle 28: After refmac, R = 0.1600 (Rfree = 0.000) for 37280 atoms. Found 162 (239 requested) and removed 142 (119 requested) atoms. Cycle 29: After refmac, R = 0.1557 (Rfree = 0.000) for 37300 atoms. Found 123 (239 requested) and removed 156 (119 requested) atoms. Cycle 30: After refmac, R = 0.1545 (Rfree = 0.000) for 37267 atoms. Found 140 (239 requested) and removed 152 (119 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38550 seeds are put forward NCS extension: 10 residues added (10 deleted due to clashes), 38560 seeds are put forward Round 1: 2763 peptides, 454 chains. Longest chain 23 peptides. Score 0.411 Round 2: 3028 peptides, 423 chains. Longest chain 29 peptides. Score 0.497 Round 3: 3079 peptides, 417 chains. Longest chain 29 peptides. Score 0.513 Round 4: 3005 peptides, 396 chains. Longest chain 24 peptides. Score 0.517 Round 5: 3001 peptides, 399 chains. Longest chain 26 peptides. Score 0.513 Taking the results from Round 4 Chains 402, Residues 2609, Estimated correctness of the model 0.0 % 11 chains (116 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10494 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1786 (Rfree = 0.000) for 37247 atoms. Found 238 (238 requested) and removed 154 (119 requested) atoms. Cycle 32: After refmac, R = 0.1718 (Rfree = 0.000) for 37331 atoms. Found 239 (239 requested) and removed 135 (119 requested) atoms. Cycle 33: After refmac, R = 0.1444 (Rfree = 0.000) for 37435 atoms. Found 26 (240 requested) and removed 128 (120 requested) atoms. Cycle 34: After refmac, R = 0.1388 (Rfree = 0.000) for 37333 atoms. Found 24 (239 requested) and removed 121 (119 requested) atoms. Cycle 35: After refmac, R = 0.1366 (Rfree = 0.000) for 37236 atoms. Found 23 (238 requested) and removed 122 (119 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 38519 seeds are put forward NCS extension: 0 residues added, 38519 seeds are put forward Round 1: 2642 peptides, 438 chains. Longest chain 20 peptides. Score 0.399 Round 2: 2929 peptides, 412 chains. Longest chain 26 peptides. Score 0.487 Round 3: 2953 peptides, 411 chains. Longest chain 28 peptides. Score 0.493 Round 4: 2983 peptides, 399 chains. Longest chain 23 peptides. Score 0.510 Round 5: 2966 peptides, 382 chains. Longest chain 32 peptides. Score 0.522 Taking the results from Round 5 Chains 397, Residues 2584, Estimated correctness of the model 0.0 % 17 chains (212 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10846 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1847 (Rfree = 0.000) for 37247 atoms. Found 213 (238 requested) and removed 159 (119 requested) atoms. Cycle 37: After refmac, R = 0.1743 (Rfree = 0.000) for 37301 atoms. Found 202 (239 requested) and removed 144 (119 requested) atoms. Cycle 38: After refmac, R = 0.1463 (Rfree = 0.000) for 37359 atoms. Found 35 (239 requested) and removed 150 (119 requested) atoms. Cycle 39: After refmac, R = 0.1399 (Rfree = 0.000) for 37244 atoms. Found 23 (238 requested) and removed 126 (119 requested) atoms. Cycle 40: After refmac, R = 0.1371 (Rfree = 0.000) for 37141 atoms. Found 20 (238 requested) and removed 120 (119 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 38325 seeds are put forward NCS extension: 0 residues added, 38325 seeds are put forward Round 1: 2533 peptides, 441 chains. Longest chain 31 peptides. Score 0.370 Round 2: 2787 peptides, 405 chains. Longest chain 19 peptides. Score 0.464 Round 3: 2876 peptides, 420 chains. Longest chain 29 peptides. Score 0.468 Round 4: 2876 peptides, 396 chains. Longest chain 33 peptides. Score 0.491 Round 5: 2875 peptides, 386 chains. Longest chain 32 peptides. Score 0.500 Taking the results from Round 5 Chains 392, Residues 2489, Estimated correctness of the model 0.0 % 10 chains (95 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 9966 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1770 (Rfree = 0.000) for 37247 atoms. Found 188 (238 requested) and removed 149 (119 requested) atoms. Cycle 42: After refmac, R = 0.1743 (Rfree = 0.000) for 37286 atoms. Found 239 (239 requested) and removed 140 (119 requested) atoms. Cycle 43: After refmac, R = 0.1700 (Rfree = 0.000) for 37385 atoms. Found 222 (239 requested) and removed 149 (119 requested) atoms. Cycle 44: After refmac, R = 0.1385 (Rfree = 0.000) for 37458 atoms. Found 25 (240 requested) and removed 141 (120 requested) atoms. Cycle 45: After refmac, R = 0.1328 (Rfree = 0.000) for 37342 atoms. Found 21 (239 requested) and removed 128 (119 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 38568 seeds are put forward NCS extension: 0 residues added, 38568 seeds are put forward Round 1: 2354 peptides, 416 chains. Longest chain 20 peptides. Score 0.353 Round 2: 2667 peptides, 390 chains. Longest chain 31 peptides. Score 0.452 Round 3: 2674 peptides, 393 chains. Longest chain 22 peptides. Score 0.451 Round 4: 2708 peptides, 388 chains. Longest chain 24 peptides. Score 0.463 Round 5: 2721 peptides, 381 chains. Longest chain 23 peptides. Score 0.473 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 391, Residues 2340, Estimated correctness of the model 0.0 % 11 chains (133 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 391 chains (2340 residues) following loop building 11 chains (133 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75179 reflections ( 93.20 % complete ) and 9523 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1761 (Rfree = 0.000) for 37247 atoms. Found 0 (238 requested) and removed 84 (119 requested) atoms. Cycle 47: After refmac, R = 0.1788 (Rfree = 0.000) for 37163 atoms. Found 0 (238 requested) and removed 114 (119 requested) atoms. Cycle 48: After refmac, R = 0.1731 (Rfree = 0.000) for 37049 atoms. Found 0 (237 requested) and removed 118 (118 requested) atoms. Cycle 49: After refmac, R = 0.1656 (Rfree = 0.000) for 36931 atoms. Found 0 (236 requested) and removed 118 (118 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 14:21:42 GMT 2018 Job finished. TimeTaking 410.8 Used memory is bytes: 22003024