Tue 25 Dec 19:27:57 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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 ============================================================ Tue 25 Dec 19:28:13 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/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-3.8-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 4485 and 0 Target number of residues in the AU: 4485 Target solvent content: 0.6566 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-3.8-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-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 82.54 63786 reflections ( 92.90 % complete ) and 0 restraints for refining 45274 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3174 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2781 (Rfree = 0.000) for 45274 atoms. Found 248 (248 requested) and removed 203 (124 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.15 Search for helices and strands: 0 residues in 0 chains, 46418 seeds are put forward NCS extension: 0 residues added, 46418 seeds are put forward Round 1: 2581 peptides, 448 chains. Longest chain 16 peptides. Score 0.375 Round 2: 3052 peptides, 400 chains. Longest chain 28 peptides. Score 0.523 Round 3: 3184 peptides, 391 chains. Longest chain 34 peptides. Score 0.556 Round 4: 3261 peptides, 380 chains. Longest chain 31 peptides. Score 0.579 Round 5: 3278 peptides, 387 chains. Longest chain 32 peptides. Score 0.576 Taking the results from Round 4 Chains 396, Residues 2881, Estimated correctness of the model 0.0 % 17 chains (205 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 12008 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2148 (Rfree = 0.000) for 37165 atoms. Found 155 (204 requested) and removed 153 (102 requested) atoms. Cycle 2: After refmac, R = 0.1986 (Rfree = 0.000) for 37167 atoms. Found 137 (204 requested) and removed 153 (102 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1867 (Rfree = 0.000) for 37151 atoms. Found 172 (204 requested) and removed 171 (102 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1486 (Rfree = 0.000) for 37152 atoms. Found 25 (204 requested) and removed 129 (102 requested) atoms. Cycle 5: After refmac, R = 0.1403 (Rfree = 0.000) for 37048 atoms. Found 12 (203 requested) and removed 133 (101 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38336 seeds are put forward NCS extension: 5 residues added (4 deleted due to clashes), 38341 seeds are put forward Round 1: 2975 peptides, 464 chains. Longest chain 21 peptides. Score 0.448 Round 2: 3255 peptides, 394 chains. Longest chain 43 peptides. Score 0.566 Round 3: 3301 peptides, 393 chains. Longest chain 40 peptides. Score 0.576 Round 4: 3348 peptides, 384 chains. Longest chain 35 peptides. Score 0.591 Round 5: 3329 peptides, 375 chains. Longest chain 42 peptides. Score 0.595 Taking the results from Round 5 Chains 396, Residues 2954, Estimated correctness of the model 0.0 % 25 chains (324 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 12705 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1989 (Rfree = 0.000) for 37165 atoms. Found 170 (204 requested) and removed 172 (102 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1848 (Rfree = 0.000) for 37163 atoms. Found 175 (204 requested) and removed 139 (102 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1764 (Rfree = 0.000) for 37199 atoms. Found 172 (204 requested) and removed 155 (102 requested) atoms. Cycle 9: After refmac, R = 0.1380 (Rfree = 0.000) for 37216 atoms. Found 24 (204 requested) and removed 149 (102 requested) atoms. Cycle 10: After refmac, R = 0.1314 (Rfree = 0.000) for 37091 atoms. Found 17 (203 requested) and removed 129 (101 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38417 seeds are put forward NCS extension: 0 residues added, 38417 seeds are put forward Round 1: 2853 peptides, 434 chains. Longest chain 23 peptides. Score 0.450 Round 2: 3185 peptides, 407 chains. Longest chain 27 peptides. Score 0.542 Round 3: 3241 peptides, 396 chains. Longest chain 29 peptides. Score 0.562 Round 4: 3229 peptides, 386 chains. Longest chain 27 peptides. Score 0.568 Round 5: 3128 peptides, 387 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 4 Chains 395, Residues 2843, Estimated correctness of the model 0.0 % 14 chains (180 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 11671 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1890 (Rfree = 0.000) for 37165 atoms. Found 172 (204 requested) and removed 157 (102 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1818 (Rfree = 0.000) for 37180 atoms. Found 192 (204 requested) and removed 157 (102 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1754 (Rfree = 0.000) for 37215 atoms. Found 188 (204 requested) and removed 170 (102 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 14: After refmac, R = 0.1665 (Rfree = 0.000) for 37233 atoms. Found 175 (204 requested) and removed 155 (102 requested) atoms. Cycle 15: After refmac, R = 0.1633 (Rfree = 0.000) for 37253 atoms. Found 188 (204 requested) and removed 182 (102 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38625 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 38644 seeds are put forward Round 1: 2749 peptides, 452 chains. Longest chain 24 peptides. Score 0.410 Round 2: 3059 peptides, 411 chains. Longest chain 28 peptides. Score 0.514 Round 3: 3120 peptides, 410 chains. Longest chain 25 peptides. Score 0.527 Round 4: 3137 peptides, 405 chains. Longest chain 28 peptides. Score 0.535 Round 5: 3135 peptides, 411 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 4 Chains 417, Residues 2732, Estimated correctness of the model 0.0 % 13 chains (147 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 11111 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1852 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 163 (102 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 17: After refmac, R = 0.1759 (Rfree = 0.000) for 37206 atoms. Found 204 (204 requested) and removed 159 (102 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1727 (Rfree = 0.000) for 37251 atoms. Found 204 (204 requested) and removed 163 (102 requested) atoms. Cycle 19: After refmac, R = 0.1280 (Rfree = 0.000) for 37292 atoms. Found 44 (205 requested) and removed 134 (102 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1206 (Rfree = 0.000) for 37202 atoms. Found 17 (204 requested) and removed 136 (102 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38478 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 38495 seeds are put forward Round 1: 2705 peptides, 453 chains. Longest chain 17 peptides. Score 0.399 Round 2: 3009 peptides, 422 chains. Longest chain 23 peptides. Score 0.494 Round 3: 3045 peptides, 423 chains. Longest chain 22 peptides. Score 0.501 Round 4: 3012 peptides, 401 chains. Longest chain 24 peptides. Score 0.514 Round 5: 3030 peptides, 394 chains. Longest chain 28 peptides. Score 0.524 Taking the results from Round 5 Chains 400, Residues 2636, Estimated correctness of the model 0.0 % 13 chains (152 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 10747 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1847 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 135 (102 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1792 (Rfree = 0.000) for 37234 atoms. Found 204 (204 requested) and removed 135 (102 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1333 (Rfree = 0.000) for 37303 atoms. Found 27 (205 requested) and removed 128 (102 requested) atoms. Cycle 24: After refmac, R = 0.1234 (Rfree = 0.000) for 37202 atoms. Found 10 (204 requested) and removed 133 (102 requested) atoms. Cycle 25: After refmac, R = 0.1218 (Rfree = 0.000) for 37079 atoms. Found 20 (203 requested) and removed 126 (101 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38309 seeds are put forward NCS extension: 0 residues added, 38309 seeds are put forward Round 1: 2536 peptides, 425 chains. Longest chain 17 peptides. Score 0.388 Round 2: 2940 peptides, 419 chains. Longest chain 30 peptides. Score 0.483 Round 3: 2977 peptides, 413 chains. Longest chain 24 peptides. Score 0.496 Round 4: 2978 peptides, 403 chains. Longest chain 36 peptides. Score 0.505 Round 5: 2994 peptides, 407 chains. Longest chain 24 peptides. Score 0.505 Taking the results from Round 5 Chains 416, Residues 2587, Estimated correctness of the model 0.0 % 13 chains (143 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 10545 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1864 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 152 (102 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1806 (Rfree = 0.000) for 37217 atoms. Found 204 (204 requested) and removed 148 (102 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1726 (Rfree = 0.000) for 37273 atoms. Found 204 (204 requested) and removed 154 (102 requested) atoms. Cycle 29: After refmac, R = 0.1742 (Rfree = 0.000) for 37323 atoms. Found 205 (205 requested) and removed 159 (102 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1657 (Rfree = 0.000) for 37369 atoms. Found 205 (205 requested) and removed 154 (102 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38718 seeds are put forward NCS extension: 0 residues added, 38718 seeds are put forward Round 1: 2494 peptides, 446 chains. Longest chain 20 peptides. Score 0.356 Round 2: 2807 peptides, 406 chains. Longest chain 27 peptides. Score 0.467 Round 3: 2833 peptides, 403 chains. Longest chain 21 peptides. Score 0.475 Round 4: 2904 peptides, 402 chains. Longest chain 28 peptides. Score 0.491 Round 5: 2886 peptides, 392 chains. Longest chain 24 peptides. Score 0.497 Taking the results from Round 5 Chains 405, Residues 2494, Estimated correctness of the model 0.0 % 21 chains (194 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 10301 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1875 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 153 (102 requested) atoms. Cycle 32: After refmac, R = 0.1790 (Rfree = 0.000) for 37216 atoms. Found 204 (204 requested) and removed 142 (102 requested) atoms. Cycle 33: After refmac, R = 0.1349 (Rfree = 0.000) for 37278 atoms. Found 34 (205 requested) and removed 131 (102 requested) atoms. Cycle 34: After refmac, R = 0.1258 (Rfree = 0.000) for 37181 atoms. Found 16 (204 requested) and removed 144 (102 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1238 (Rfree = 0.000) for 37053 atoms. Found 24 (203 requested) and removed 124 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38246 seeds are put forward NCS extension: 0 residues added, 38246 seeds are put forward Round 1: 2436 peptides, 442 chains. Longest chain 26 peptides. Score 0.346 Round 2: 2739 peptides, 429 chains. Longest chain 20 peptides. Score 0.430 Round 3: 2731 peptides, 414 chains. Longest chain 21 peptides. Score 0.443 Round 4: 2749 peptides, 412 chains. Longest chain 28 peptides. Score 0.449 Round 5: 2770 peptides, 393 chains. Longest chain 23 peptides. Score 0.471 Taking the results from Round 5 Chains 399, Residues 2377, Estimated correctness of the model 0.0 % 7 chains (76 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63786 reflections ( 92.90 % complete ) and 9361 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1872 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 133 (102 requested) atoms. Cycle 37: After refmac, R = 0.1787 (Rfree = 0.000) for 37236 atoms. Found 204 (204 requested) and removed 133 (102 requested) atoms. Cycle 38: After refmac, R = 0.1314 (Rfree = 0.000) for 37307 atoms. Found 37 (205 requested) and removed 126 (102 requested) atoms. Cycle 39: After refmac, R = 0.1224 (Rfree = 0.000) for 37218 atoms. Found 25 (204 requested) and removed 133 (102 requested) atoms. Cycle 40: After refmac, R = 0.1195 (Rfree = 0.000) for 37110 atoms. Found 24 (204 requested) and removed 122 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38203 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 38216 seeds are put forward Round 1: 2272 peptides, 416 chains. Longest chain 21 peptides. Score 0.333 Round 2: 2584 peptides, 417 chains. Longest chain 23 peptides. Score 0.407 Round 3: 2630 peptides, 409 chains. Longest chain 27 peptides. Score 0.425 Round 4: 2635 peptides, 399 chains. Longest chain 28 peptides. Score 0.436 Round 5: 2712 peptides, 413 chains. Longest chain 26 peptides. Score 0.440 Taking the results from Round 5 Chains 416, Residues 2299, Estimated correctness of the model 0.0 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 9078 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1824 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 133 (102 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1779 (Rfree = 0.000) for 37236 atoms. Found 204 (204 requested) and removed 136 (102 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1762 (Rfree = 0.000) for 37304 atoms. Found 205 (205 requested) and removed 158 (102 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1231 (Rfree = 0.000) for 37351 atoms. Found 32 (205 requested) and removed 125 (102 requested) atoms. Cycle 45: After refmac, R = 0.1153 (Rfree = 0.000) for 37258 atoms. Found 28 (204 requested) and removed 129 (102 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38420 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 38440 seeds are put forward Round 1: 2081 peptides, 400 chains. Longest chain 28 peptides. Score 0.302 Round 2: 2525 peptides, 413 chains. Longest chain 20 peptides. Score 0.397 Round 3: 2560 peptides, 402 chains. Longest chain 27 peptides. Score 0.416 Round 4: 2581 peptides, 385 chains. Longest chain 24 peptides. Score 0.438 Round 5: 2570 peptides, 389 chains. Longest chain 29 peptides. Score 0.432 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 395, Residues 2196, Estimated correctness of the model 0.0 % 8 chains (80 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 395 chains (2196 residues) following loop building 8 chains (80 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63786 reflections ( 92.90 % complete ) and 8741 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1742 (Rfree = 0.000) for 37165 atoms. Found 0 (204 requested) and removed 102 (102 requested) atoms. Cycle 47: After refmac, R = 0.1750 (Rfree = 0.000) for 37063 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1672 (Rfree = 0.000) for 36962 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1194 (Rfree = 0.000) for 36861 atoms. Found 0 (202 requested) and removed 101 (101 requested) atoms. Writing output files ... TimeTaking 473.7