Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pnk-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.6-parrot-hancs/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-hancs.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-hancs.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 45551 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3078 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2624 (Rfree = 0.000) for 45551 atoms. Found 292 (292 requested) and removed 207 (146 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.02 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: 2788 peptides, 473 chains. Longest chain 21 peptides. Score 0.398 Round 2: 3268 peptides, 431 chains. Longest chain 30 peptides. Score 0.537 Round 3: 3372 peptides, 416 chains. Longest chain 38 peptides. Score 0.569 Round 4: 3433 peptides, 392 chains. Longest chain 38 peptides. Score 0.599 Round 5: 3463 peptides, 387 chains. Longest chain 36 peptides. Score 0.609 Taking the results from Round 5 Chains 407, Residues 3076, Estimated correctness of the model 18.1 % 21 chains (317 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 13208 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2069 (Rfree = 0.000) for 37247 atoms. Found 179 (238 requested) and removed 167 (119 requested) atoms. Cycle 2: After refmac, R = 0.1926 (Rfree = 0.000) for 37259 atoms. Found 135 (239 requested) and removed 155 (119 requested) atoms. Cycle 3: After refmac, R = 0.1826 (Rfree = 0.000) for 37239 atoms. Found 116 (238 requested) and removed 170 (119 requested) atoms. Cycle 4: After refmac, R = 0.1714 (Rfree = 0.000) for 37185 atoms. Found 91 (238 requested) and removed 170 (119 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1463 (Rfree = 0.000) for 37106 atoms. Found 26 (238 requested) and removed 148 (119 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38470 seeds are put forward NCS extension: 37 residues added (15 deleted due to clashes), 38507 seeds are put forward Round 1: 3207 peptides, 449 chains. Longest chain 30 peptides. Score 0.510 Round 2: 3425 peptides, 391 chains. Longest chain 47 peptides. Score 0.599 Round 3: 3428 peptides, 394 chains. Longest chain 34 peptides. Score 0.597 Round 4: 3445 peptides, 388 chains. Longest chain 58 peptides. Score 0.605 Round 5: 3455 peptides, 373 chains. Longest chain 46 peptides. Score 0.618 Taking the results from Round 5 Chains 403, Residues 3082, Estimated correctness of the model 21.6 % 27 chains (426 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 13750 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1952 (Rfree = 0.000) for 37247 atoms. Found 169 (238 requested) and removed 186 (119 requested) atoms. Cycle 7: After refmac, R = 0.1852 (Rfree = 0.000) for 37230 atoms. Found 159 (238 requested) and removed 156 (119 requested) atoms. Cycle 8: After refmac, R = 0.1778 (Rfree = 0.000) for 37233 atoms. Found 126 (238 requested) and removed 145 (119 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1714 (Rfree = 0.000) for 37214 atoms. Found 130 (238 requested) and removed 159 (119 requested) atoms. Cycle 10: After refmac, R = 0.1653 (Rfree = 0.000) for 37185 atoms. Found 91 (238 requested) and removed 162 (119 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38467 seeds are put forward NCS extension: 28 residues added (7 deleted due to clashes), 38495 seeds are put forward Round 1: 3088 peptides, 431 chains. Longest chain 24 peptides. Score 0.502 Round 2: 3356 peptides, 397 chains. Longest chain 49 peptides. Score 0.582 Round 3: 3358 peptides, 384 chains. Longest chain 34 peptides. Score 0.593 Round 4: 3367 peptides, 390 chains. Longest chain 31 peptides. Score 0.590 Round 5: 3344 peptides, 383 chains. Longest chain 33 peptides. Score 0.591 Taking the results from Round 3 Chains 405, Residues 2974, Estimated correctness of the model 11.9 % 23 chains (315 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12806 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1880 (Rfree = 0.000) for 37247 atoms. Found 169 (238 requested) and removed 175 (119 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1785 (Rfree = 0.000) for 37241 atoms. Found 153 (238 requested) and removed 150 (119 requested) atoms. Cycle 13: After refmac, R = 0.1719 (Rfree = 0.000) for 37244 atoms. Found 118 (238 requested) and removed 153 (119 requested) atoms. Cycle 14: After refmac, R = 0.1645 (Rfree = 0.000) for 37209 atoms. Found 87 (238 requested) and removed 150 (119 requested) atoms. Cycle 15: After refmac, R = 0.1604 (Rfree = 0.000) for 37146 atoms. Found 107 (238 requested) and removed 161 (119 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 38434 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 38451 seeds are put forward Round 1: 3050 peptides, 444 chains. Longest chain 23 peptides. Score 0.482 Round 2: 3334 peptides, 413 chains. Longest chain 28 peptides. Score 0.565 Round 3: 3378 peptides, 397 chains. Longest chain 42 peptides. Score 0.586 Round 4: 3352 peptides, 396 chains. Longest chain 38 peptides. Score 0.582 Round 5: 3303 peptides, 390 chains. Longest chain 35 peptides. Score 0.578 Taking the results from Round 3 Chains 418, Residues 2981, Estimated correctness of the model 9.1 % 30 chains (474 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 13470 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1839 (Rfree = 0.000) for 37247 atoms. Found 191 (238 requested) and removed 189 (119 requested) atoms. Cycle 17: After refmac, R = 0.1714 (Rfree = 0.000) for 37249 atoms. Found 120 (238 requested) and removed 162 (119 requested) atoms. Cycle 18: After refmac, R = 0.1655 (Rfree = 0.000) for 37207 atoms. Found 103 (238 requested) and removed 146 (119 requested) atoms. Cycle 19: After refmac, R = 0.1604 (Rfree = 0.000) for 37164 atoms. Found 90 (238 requested) and removed 162 (119 requested) atoms. Cycle 20: After refmac, R = 0.1561 (Rfree = 0.000) for 37092 atoms. Found 93 (237 requested) and removed 156 (118 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38332 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 38354 seeds are put forward Round 1: 3022 peptides, 446 chains. Longest chain 26 peptides. Score 0.475 Round 2: 3212 peptides, 400 chains. Longest chain 31 peptides. Score 0.553 Round 3: 3288 peptides, 413 chains. Longest chain 29 peptides. Score 0.556 Round 4: 3311 peptides, 389 chains. Longest chain 32 peptides. Score 0.581 Round 5: 3263 peptides, 384 chains. Longest chain 35 peptides. Score 0.576 Taking the results from Round 4 Chains 408, Residues 2922, Estimated correctness of the model 7.1 % 23 chains (289 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 12464 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1839 (Rfree = 0.000) for 37247 atoms. Found 162 (238 requested) and removed 181 (119 requested) atoms. Cycle 22: After refmac, R = 0.1741 (Rfree = 0.000) for 37228 atoms. Found 166 (238 requested) and removed 155 (119 requested) atoms. Cycle 23: After refmac, R = 0.1662 (Rfree = 0.000) for 37239 atoms. Found 98 (238 requested) and removed 144 (119 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1590 (Rfree = 0.000) for 37193 atoms. Found 92 (238 requested) and removed 149 (119 requested) atoms. Cycle 25: After refmac, R = 0.1558 (Rfree = 0.000) for 37136 atoms. Found 122 (238 requested) and removed 149 (119 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38360 seeds are put forward NCS extension: 0 residues added, 38360 seeds are put forward Round 1: 2905 peptides, 444 chains. Longest chain 21 peptides. Score 0.452 Round 2: 3146 peptides, 420 chains. Longest chain 34 peptides. Score 0.523 Round 3: 3210 peptides, 409 chains. Longest chain 46 peptides. Score 0.545 Round 4: 3200 peptides, 412 chains. Longest chain 28 peptides. Score 0.541 Round 5: 3187 peptides, 403 chains. Longest chain 35 peptides. Score 0.546 Taking the results from Round 5 Chains 422, Residues 2784, Estimated correctness of the model 0.0 % 20 chains (241 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 75179 reflections ( 93.20 % complete ) and 11685 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1837 (Rfree = 0.000) for 37247 atoms. Found 168 (238 requested) and removed 159 (119 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1716 (Rfree = 0.000) for 37256 atoms. Found 140 (239 requested) and removed 155 (119 requested) atoms. Cycle 28: After refmac, R = 0.1655 (Rfree = 0.000) for 37241 atoms. Found 121 (238 requested) and removed 155 (119 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1373 (Rfree = 0.000) for 37207 atoms. Found 28 (238 requested) and removed 140 (119 requested) atoms. Cycle 30: After refmac, R = 0.1322 (Rfree = 0.000) for 37095 atoms. Found 20 (237 requested) and removed 131 (118 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 38303 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 38324 seeds are put forward Round 1: 2846 peptides, 464 chains. Longest chain 20 peptides. Score 0.420 Round 2: 3122 peptides, 422 chains. Longest chain 33 peptides. Score 0.517 Round 3: 3164 peptides, 419 chains. Longest chain 29 peptides. Score 0.528 Round 4: 3128 peptides, 399 chains. Longest chain 43 peptides. Score 0.538 Round 5: 3172 peptides, 404 chains. Longest chain 30 peptides. Score 0.542 Taking the results from Round 5 Chains 418, Residues 2768, Estimated correctness of the model 0.0 % 19 chains (215 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 11547 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1808 (Rfree = 0.000) for 37247 atoms. Found 164 (238 requested) and removed 159 (119 requested) atoms. Cycle 32: After refmac, R = 0.1706 (Rfree = 0.000) for 37252 atoms. Found 179 (238 requested) and removed 142 (119 requested) atoms. Cycle 33: After refmac, R = 0.1675 (Rfree = 0.000) for 37289 atoms. Found 176 (239 requested) and removed 148 (119 requested) atoms. Cycle 34: After refmac, R = 0.1599 (Rfree = 0.000) for 37317 atoms. Found 123 (239 requested) and removed 148 (119 requested) atoms. Cycle 35: After refmac, R = 0.1595 (Rfree = 0.000) for 37292 atoms. Found 161 (239 requested) and removed 147 (119 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38529 seeds are put forward NCS extension: 4 residues added (3 deleted due to clashes), 38533 seeds are put forward Round 1: 2592 peptides, 440 chains. Longest chain 23 peptides. Score 0.385 Round 2: 2947 peptides, 414 chains. Longest chain 30 peptides. Score 0.489 Round 3: 3004 peptides, 401 chains. Longest chain 29 peptides. Score 0.512 Round 4: 2966 peptides, 402 chains. Longest chain 32 peptides. Score 0.504 Round 5: 3019 peptides, 408 chains. Longest chain 31 peptides. Score 0.509 Taking the results from Round 3 Chains 409, Residues 2603, Estimated correctness of the model 0.0 % 18 chains (177 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10708 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1760 (Rfree = 0.000) for 37247 atoms. Found 175 (238 requested) and removed 152 (119 requested) atoms. Cycle 37: After refmac, R = 0.1687 (Rfree = 0.000) for 37270 atoms. Found 138 (239 requested) and removed 153 (119 requested) atoms. Cycle 38: After refmac, R = 0.1643 (Rfree = 0.000) for 37255 atoms. Found 143 (239 requested) and removed 149 (119 requested) atoms. Cycle 39: After refmac, R = 0.1588 (Rfree = 0.000) for 37249 atoms. Found 139 (238 requested) and removed 154 (119 requested) atoms. Cycle 40: After refmac, R = 0.1301 (Rfree = 0.000) for 37234 atoms. Found 28 (238 requested) and removed 132 (119 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38333 seeds are put forward NCS extension: 0 residues added, 38333 seeds are put forward Round 1: 2523 peptides, 449 chains. Longest chain 17 peptides. Score 0.360 Round 2: 2843 peptides, 408 chains. Longest chain 35 peptides. Score 0.473 Round 3: 2905 peptides, 420 chains. Longest chain 27 peptides. Score 0.474 Round 4: 2955 peptides, 426 chains. Longest chain 30 peptides. Score 0.479 Round 5: 2935 peptides, 411 chains. Longest chain 27 peptides. Score 0.489 Taking the results from Round 5 Chains 426, Residues 2524, Estimated correctness of the model 0.0 % 21 chains (257 residues) have been docked in sequence ------------------------------------------------------ 75179 reflections ( 93.20 % complete ) and 10736 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1749 (Rfree = 0.000) for 37247 atoms. Found 161 (238 requested) and removed 166 (119 requested) atoms. Cycle 42: After refmac, R = 0.1654 (Rfree = 0.000) for 37242 atoms. Found 145 (238 requested) and removed 148 (119 requested) atoms. Cycle 43: After refmac, R = 0.1616 (Rfree = 0.000) for 37239 atoms. Found 135 (238 requested) and removed 153 (119 requested) atoms. Cycle 44: After refmac, R = 0.1553 (Rfree = 0.000) for 37221 atoms. Found 125 (238 requested) and removed 153 (119 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1292 (Rfree = 0.000) for 37193 atoms. Found 32 (238 requested) and removed 145 (119 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 2.99 Search for helices and strands: 0 residues in 0 chains, 38338 seeds are put forward NCS extension: 0 residues added, 38338 seeds are put forward Round 1: 2467 peptides, 428 chains. Longest chain 19 peptides. Score 0.368 Round 2: 2774 peptides, 419 chains. Longest chain 24 peptides. Score 0.447 Round 3: 2787 peptides, 395 chains. Longest chain 27 peptides. Score 0.473 Round 4: 2861 peptides, 409 chains. Longest chain 31 peptides. Score 0.476 Round 5: 2851 peptides, 408 chains. Longest chain 21 peptides. Score 0.474 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 415, Residues 2452, Estimated correctness of the model 0.0 % 13 chains (118 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 415 chains (2452 residues) following loop building 13 chains (118 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75179 reflections ( 93.20 % complete ) and 9826 restraints for refining 37247 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1696 (Rfree = 0.000) for 37247 atoms. Found 0 (238 requested) and removed 95 (119 requested) atoms. Cycle 47: After refmac, R = 0.1689 (Rfree = 0.000) for 37152 atoms. Found 0 (238 requested) and removed 81 (119 requested) atoms. Cycle 48: After refmac, R = 0.1619 (Rfree = 0.000) for 37071 atoms. Found 0 (237 requested) and removed 118 (118 requested) atoms. Cycle 49: After refmac, R = 0.1587 (Rfree = 0.000) for 36953 atoms. Found 0 (237 requested) and removed 118 (118 requested) atoms. Writing output files ... TimeTaking 403.07