Starting phenix.real_space_refine on Mon Jul 6 00:19:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szj_25570/07_2026/7szj_25570.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 106 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19211 2.51 5 N 5523 2.21 5 O 6202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31173 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 4, 'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3799 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 14, 'TRANS': 451} Chain breaks: 3 Chain: "X" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1162 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "Y" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'RFP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14615 SG CYS D 70 64.628 116.508 81.516 1.00 34.65 S ATOM 14629 SG CYS D 72 64.329 116.955 85.439 1.00 36.54 S ATOM 14737 SG CYS D 85 63.760 119.837 83.215 1.00 39.22 S ATOM 14761 SG CYS D 88 67.167 118.538 83.641 1.00 40.02 S ATOM 20449 SG CYS D 814 101.537 96.654 28.039 1.00 28.16 S ATOM 21014 SG CYS D 888 102.173 96.436 31.666 1.00 23.24 S ATOM 21065 SG CYS D 895 100.123 93.940 30.058 1.00 14.89 S ATOM 21086 SG CYS D 898 103.580 94.008 29.413 1.00 15.21 S Time building chain proxies: 6.21, per 1000 atoms: 0.20 Number of scatterers: 31173 At special positions: 0 Unit cell: (192.64, 191.52, 165.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 106 15.00 Mg 1 11.99 O 6202 8.00 N 5523 7.00 C 19211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 48 sheets defined 44.4% alpha, 14.0% beta 23 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.892A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.773A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.603A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.749A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.731A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.554A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.978A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.436A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.715A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.959A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.079A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.936A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.511A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.827A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.576A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.070A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.558A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 removed outlier: 4.325A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.817A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 4.033A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 removed outlier: 3.778A pdb=" N VAL C 650 " --> pdb=" O ARG C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.578A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.244A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 995 through 1000 removed outlier: 3.762A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.840A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.649A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.415A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.570A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.659A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.509A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.670A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.952A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.617A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.589A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.501A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.035A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.760A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 332' Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.740A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.898A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.567A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.089A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.961A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.504A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.868A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.656A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.438A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 removed outlier: 3.695A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.871A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.562A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.870A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.757A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.517A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.937A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 removed outlier: 3.659A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 152 Processing helix chain 'F' and resid 157 through 161 Processing helix chain 'F' and resid 214 through 234 Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.672A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.578A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.728A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.308A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.180A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 492 through 500 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.621A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 553 through 563 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 585 through 600 Processing helix chain 'F' and resid 604 through 611 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.581A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.508A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.562A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 17 removed outlier: 4.351A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 7.917A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.632A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.905A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.878A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.878A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.555A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.331A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.555A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.412A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.801A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.295A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.422A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.746A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.751A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.710A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD9, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AE1, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 3.675A pdb=" N VAL D 858 " --> pdb=" O VAL D 848 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 952 removed outlier: 7.188A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.552A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.636A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1187 through 1188 Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AF3, first strand: chain 'F' and resid 162 through 165 removed outlier: 5.696A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 8.01 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5190 1.30 - 1.43: 7911 1.43 - 1.56: 18315 1.56 - 1.69: 217 1.69 - 1.81: 225 Bond restraints: 31858 Sorted by residual: bond pdb=" C6 RFP C3001 " pdb=" O3 RFP C3001 " ideal model delta sigma weight residual 1.339 1.531 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" C6 RFP C3001 " pdb=" C7 RFP C3001 " ideal model delta sigma weight residual 1.387 1.570 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" C10 RFP C3001 " pdb=" C4 RFP C3001 " ideal model delta sigma weight residual 1.411 1.572 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C1 RFP C3001 " pdb=" C9 RFP C3001 " ideal model delta sigma weight residual 1.411 1.570 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C10 RFP C3001 " pdb=" C5 RFP C3001 " ideal model delta sigma weight residual 1.431 1.590 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 31853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 42825 2.02 - 4.05: 592 4.05 - 6.07: 42 6.07 - 8.10: 4 8.10 - 10.12: 7 Bond angle restraints: 43470 Sorted by residual: angle pdb=" N3 DT Y 44 " pdb=" C4 DT Y 44 " pdb=" O4 DT Y 44 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N PHE D1274 " pdb=" CA PHE D1274 " pdb=" CB PHE D1274 " ideal model delta sigma weight residual 114.17 109.49 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" N3 DT X 52 " pdb=" C4 DT X 52 " pdb=" O4 DT X 52 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT Y 51 " pdb=" C4 DT Y 51 " pdb=" O4 DT Y 51 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT X 39 " pdb=" C4 DT X 39 " pdb=" O4 DT X 39 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 43465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 18628 35.37 - 70.74: 709 70.74 - 106.11: 30 106.11 - 141.48: 7 141.48 - 176.85: 2 Dihedral angle restraints: 19376 sinusoidal: 8772 harmonic: 10604 Sorted by residual: dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 140.07 39.93 0 5.00e+00 4.00e-02 6.38e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 19373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4373 0.067 - 0.133: 569 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C22 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C32 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.47 2.80 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C24 RFP C3001 " pdb=" C23 RFP C3001 " pdb=" C25 RFP C3001 " pdb=" C33 RFP C3001 " both_signs ideal model delta sigma weight residual False 2.56 2.79 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C20 RFP C3001 " pdb=" C19 RFP C3001 " pdb=" C21 RFP C3001 " pdb=" C31 RFP C3001 " both_signs ideal model delta sigma weight residual False -2.56 -2.77 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4949 not shown) Planarity restraints: 5309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 697 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO C 698 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 178 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 179 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 104 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU F 104 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU F 104 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 5306 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 241 2.56 - 3.15: 26149 3.15 - 3.73: 46058 3.73 - 4.32: 64050 4.32 - 4.90: 108682 Nonbonded interactions: 245180 Sorted by model distance: nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 1.979 3.040 nonbonded pdb=" OE1 GLU D1030 " pdb=" OH TYR D1099 " model vdw 1.996 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" O ILE C 138 " model vdw 2.015 3.040 nonbonded pdb=" OG1 THR C 843 " pdb=" O GLY C 846 " model vdw 2.024 3.040 nonbonded pdb=" O LEU C 397 " pdb=" OG SER C 398 " model vdw 2.060 3.040 ... (remaining 245175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 31866 Z= 0.300 Angle : 0.561 10.124 43482 Z= 0.347 Chirality : 0.042 0.333 4952 Planarity : 0.004 0.061 5309 Dihedral : 17.127 176.854 12540 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3661 helix: 2.13 (0.14), residues: 1461 sheet: -0.30 (0.27), residues: 390 loop : -1.48 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 476 TYR 0.013 0.001 TYR D 631 PHE 0.019 0.001 PHE C 514 TRP 0.008 0.001 TRP F 326 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.29 (31858) covalent geometry : angle 0.56090 / 0.35 (43470) hydrogen bonds : bond 0.17940 / 12.53 ( 1358) hydrogen bonds : angle 6.66424 / 4.66 ( 3828) metal coordination : bond 0.10899 / 5.36 ( 8) metal coordination : angle 0.98185 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.9007 (mmp) cc_final: 0.8481 (mmp) REVERT: C 1315 MET cc_start: 0.8477 (ptt) cc_final: 0.8249 (ptt) REVERT: D 697 MET cc_start: 0.8668 (ttp) cc_final: 0.8446 (ttp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2295 time to fit residues: 104.0143 Evaluate side-chains 251 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 0.0060 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.2980 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 23 HIS B 127 GLN C 69 GLN C 330 HIS ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D1197 ASN F 227 GLN F 294 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.183292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142127 restraints weight = 36492.885| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.52 r_work: 0.3167 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31866 Z= 0.138 Angle : 0.640 10.704 43482 Z= 0.335 Chirality : 0.045 0.265 4952 Planarity : 0.004 0.058 5309 Dihedral : 16.421 179.945 5261 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 0.57 % Allowed : 7.92 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3661 helix: 1.92 (0.14), residues: 1479 sheet: -0.18 (0.26), residues: 411 loop : -1.30 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 245 TYR 0.026 0.001 TYR D 46 PHE 0.016 0.001 PHE D 172 TRP 0.029 0.001 TRP F 433 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (31858) covalent geometry : angle 0.63803 / 0.34 (43470) hydrogen bonds : bond 0.05557 / 3.91 ( 1358) hydrogen bonds : angle 4.81668 / 3.35 ( 3828) metal coordination : bond 0.01128 / 0.59 ( 8) metal coordination : angle 3.25923 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 1.169 Fit side-chains REVERT: A 51 MET cc_start: 0.9013 (mmp) cc_final: 0.8452 (mmp) REVERT: A 229 GLU cc_start: 0.7992 (pp20) cc_final: 0.7673 (pt0) REVERT: B 16 ILE cc_start: 0.8517 (mp) cc_final: 0.8304 (mt) REVERT: B 191 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7992 (ptt180) REVERT: C 485 ASP cc_start: 0.6008 (p0) cc_final: 0.5788 (p0) REVERT: D 697 MET cc_start: 0.8878 (ttp) cc_final: 0.8425 (ttp) REVERT: F 294 GLN cc_start: 0.1459 (OUTLIER) cc_final: 0.1108 (mp10) outliers start: 18 outliers final: 11 residues processed: 293 average time/residue: 0.2124 time to fit residues: 99.7855 Evaluate side-chains 260 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain F residue 294 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 331 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 370 optimal weight: 20.0000 chunk 354 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 294 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN F 227 GLN ** F 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132324 restraints weight = 36302.298| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.92 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31866 Z= 0.253 Angle : 0.700 10.925 43482 Z= 0.364 Chirality : 0.047 0.208 4952 Planarity : 0.006 0.071 5309 Dihedral : 16.530 179.260 5261 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 1.27 % Allowed : 11.70 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3661 helix: 1.63 (0.14), residues: 1476 sheet: -0.24 (0.26), residues: 423 loop : -1.56 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 45 TYR 0.019 0.002 TYR D 46 PHE 0.022 0.002 PHE C 514 TRP 0.021 0.002 TRP F 433 HIS 0.009 0.002 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.25 (31858) covalent geometry : angle 0.69619 / 0.36 (43470) hydrogen bonds : bond 0.06649 / 4.68 ( 1358) hydrogen bonds : angle 4.70144 / 3.26 ( 3828) metal coordination : bond 0.01148 / 0.56 ( 8) metal coordination : angle 4.15557 / 2.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.977 Fit side-chains REVERT: A 51 MET cc_start: 0.8826 (mmp) cc_final: 0.8287 (mmp) REVERT: D 129 ASP cc_start: 0.6980 (t0) cc_final: 0.6756 (t0) outliers start: 40 outliers final: 24 residues processed: 285 average time/residue: 0.2143 time to fit residues: 97.4672 Evaluate side-chains 266 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 494 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 13 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 375 optimal weight: 50.0000 chunk 219 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 952 GLN D1098 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 331 HIS F 338 HIS ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133466 restraints weight = 36284.068| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.99 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31866 Z= 0.164 Angle : 0.609 10.378 43482 Z= 0.320 Chirality : 0.044 0.217 4952 Planarity : 0.005 0.061 5309 Dihedral : 16.487 178.920 5261 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.65 % Allowed : 13.29 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3661 helix: 1.73 (0.14), residues: 1473 sheet: -0.17 (0.26), residues: 416 loop : -1.54 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 542 TYR 0.019 0.001 TYR D 46 PHE 0.015 0.001 PHE C 514 TRP 0.011 0.001 TRP F 326 HIS 0.005 0.001 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (31858) covalent geometry : angle 0.60681 / 0.32 (43470) hydrogen bonds : bond 0.05505 / 3.88 ( 1358) hydrogen bonds : angle 4.51470 / 3.13 ( 3828) metal coordination : bond 0.00705 / 0.35 ( 8) metal coordination : angle 3.42840 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 1.090 Fit side-chains REVERT: A 51 MET cc_start: 0.8650 (mmp) cc_final: 0.7656 (mmp) REVERT: C 866 ASP cc_start: 0.8932 (p0) cc_final: 0.8622 (p0) REVERT: D 81 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6877 (mtm-85) REVERT: D 129 ASP cc_start: 0.7106 (t0) cc_final: 0.6841 (t0) REVERT: D 151 MET cc_start: 0.7318 (pmm) cc_final: 0.6871 (pmm) REVERT: D 664 ILE cc_start: 0.7643 (mm) cc_final: 0.7396 (tt) REVERT: D 697 MET cc_start: 0.8750 (ttp) cc_final: 0.8404 (ttp) REVERT: F 294 GLN cc_start: 0.1779 (OUTLIER) cc_final: 0.1359 (mt0) outliers start: 52 outliers final: 28 residues processed: 295 average time/residue: 0.2131 time to fit residues: 101.0094 Evaluate side-chains 275 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 494 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 149 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 370 optimal weight: 30.0000 chunk 328 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132591 restraints weight = 36086.313| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.90 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 31866 Z= 0.231 Angle : 0.665 10.117 43482 Z= 0.347 Chirality : 0.046 0.227 4952 Planarity : 0.005 0.061 5309 Dihedral : 16.476 179.205 5261 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 2.16 % Allowed : 14.79 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3661 helix: 1.59 (0.13), residues: 1471 sheet: -0.34 (0.25), residues: 422 loop : -1.63 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.015 0.002 TYR D 46 PHE 0.017 0.002 PHE C 514 TRP 0.021 0.002 TRP F 433 HIS 0.010 0.002 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.23 (31858) covalent geometry : angle 0.66151 / 0.35 (43470) hydrogen bonds : bond 0.06223 / 4.39 ( 1358) hydrogen bonds : angle 4.54186 / 3.15 ( 3828) metal coordination : bond 0.00858 / 0.42 ( 8) metal coordination : angle 3.91570 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8762 (mmp) cc_final: 0.8159 (mmp) REVERT: C 800 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: C 866 ASP cc_start: 0.8970 (p0) cc_final: 0.8670 (p0) REVERT: C 1160 ASP cc_start: 0.5929 (OUTLIER) cc_final: 0.4807 (p0) REVERT: D 81 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6875 (mtm-85) REVERT: D 129 ASP cc_start: 0.7047 (t0) cc_final: 0.6715 (t0) REVERT: D 151 MET cc_start: 0.7134 (pmm) cc_final: 0.6841 (pmm) REVERT: D 664 ILE cc_start: 0.7711 (mm) cc_final: 0.7503 (tt) REVERT: D 697 MET cc_start: 0.8776 (ttp) cc_final: 0.8464 (ttp) REVERT: D 1196 LEU cc_start: 0.8172 (mp) cc_final: 0.7918 (mp) REVERT: F 104 GLU cc_start: 0.7414 (mp0) cc_final: 0.7189 (mp0) outliers start: 68 outliers final: 42 residues processed: 303 average time/residue: 0.2055 time to fit residues: 100.1183 Evaluate side-chains 292 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 567 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 55 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 146 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 368 optimal weight: 50.0000 chunk 326 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 271 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135976 restraints weight = 35864.960| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.82 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31866 Z= 0.122 Angle : 0.557 8.433 43482 Z= 0.297 Chirality : 0.042 0.237 4952 Planarity : 0.004 0.062 5309 Dihedral : 16.323 179.466 5261 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.46 % Allowed : 15.90 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3661 helix: 1.83 (0.14), residues: 1473 sheet: -0.17 (0.26), residues: 416 loop : -1.47 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 608 TYR 0.016 0.001 TYR D 46 PHE 0.009 0.001 PHE C 505 TRP 0.016 0.001 TRP F 433 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (31858) covalent geometry : angle 0.55485 / 0.30 (43470) hydrogen bonds : bond 0.04726 / 3.32 ( 1358) hydrogen bonds : angle 4.33341 / 3.01 ( 3828) metal coordination : bond 0.00535 / 0.27 ( 8) metal coordination : angle 2.92061 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 1.095 Fit side-chains REVERT: C 145 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8645 (mm) REVERT: C 866 ASP cc_start: 0.8877 (p0) cc_final: 0.8596 (p0) REVERT: C 1340 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7409 (mm-30) REVERT: D 129 ASP cc_start: 0.7018 (t0) cc_final: 0.6670 (t0) REVERT: D 227 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7590 (t80) REVERT: D 697 MET cc_start: 0.8695 (ttp) cc_final: 0.8371 (ttp) REVERT: D 1196 LEU cc_start: 0.8127 (mp) cc_final: 0.7880 (mp) outliers start: 46 outliers final: 33 residues processed: 301 average time/residue: 0.2087 time to fit residues: 100.5560 Evaluate side-chains 286 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 283 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 187 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.182058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132118 restraints weight = 36256.305| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.95 r_work: 0.2863 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31866 Z= 0.154 Angle : 0.580 7.919 43482 Z= 0.305 Chirality : 0.043 0.226 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.247 178.884 5261 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.07 % Allowed : 16.03 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3661 helix: 1.82 (0.14), residues: 1470 sheet: -0.13 (0.25), residues: 418 loop : -1.52 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1033 TYR 0.014 0.001 TYR D 46 PHE 0.012 0.001 PHE D1319 TRP 0.019 0.001 TRP F 433 HIS 0.006 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (31858) covalent geometry : angle 0.57791 / 0.31 (43470) hydrogen bonds : bond 0.05108 / 3.60 ( 1358) hydrogen bonds : angle 4.30464 / 2.99 ( 3828) metal coordination : bond 0.00595 / 0.30 ( 8) metal coordination : angle 3.15385 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 1.288 Fit side-chains REVERT: B 170 ARG cc_start: 0.6740 (ttm110) cc_final: 0.6116 (ttm-80) REVERT: C 145 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 631 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: C 800 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8012 (mtp) REVERT: C 866 ASP cc_start: 0.8827 (p0) cc_final: 0.8571 (p0) REVERT: D 81 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7102 (mtm-85) REVERT: D 129 ASP cc_start: 0.7934 (t0) cc_final: 0.7540 (t0) REVERT: D 227 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7395 (t80) REVERT: D 697 MET cc_start: 0.8969 (ttp) cc_final: 0.8588 (ttp) outliers start: 65 outliers final: 44 residues processed: 301 average time/residue: 0.2128 time to fit residues: 102.8213 Evaluate side-chains 298 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 242 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 chunk 371 optimal weight: 20.0000 chunk 315 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.179331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131670 restraints weight = 36235.589| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.91 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31866 Z= 0.252 Angle : 0.668 9.757 43482 Z= 0.348 Chirality : 0.046 0.211 4952 Planarity : 0.005 0.060 5309 Dihedral : 16.334 178.640 5261 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.74 % Rotamer: Outliers : 2.26 % Allowed : 16.41 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3661 helix: 1.61 (0.13), residues: 1468 sheet: -0.19 (0.25), residues: 421 loop : -1.66 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 45 TYR 0.015 0.002 TYR D 631 PHE 0.022 0.002 PHE A 35 TRP 0.020 0.002 TRP F 433 HIS 0.010 0.002 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.25 (31858) covalent geometry : angle 0.66549 / 0.35 (43470) hydrogen bonds : bond 0.06240 / 4.39 ( 1358) hydrogen bonds : angle 4.42960 / 3.07 ( 3828) metal coordination : bond 0.00872 / 0.43 ( 8) metal coordination : angle 3.73689 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: C 145 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8518 (mm) REVERT: C 631 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: C 800 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7746 (mtp) REVERT: C 866 ASP cc_start: 0.9030 (p0) cc_final: 0.8684 (p0) REVERT: C 1160 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.4705 (p0) REVERT: C 1340 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 81 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6850 (mtm-85) REVERT: D 129 ASP cc_start: 0.7027 (t0) cc_final: 0.6743 (t0) REVERT: D 151 MET cc_start: 0.7336 (pmm) cc_final: 0.7129 (pmm) REVERT: D 227 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7708 (t80) REVERT: D 664 ILE cc_start: 0.7713 (mm) cc_final: 0.7472 (tt) REVERT: D 697 MET cc_start: 0.8820 (ttp) cc_final: 0.8514 (ttp) outliers start: 71 outliers final: 51 residues processed: 299 average time/residue: 0.2084 time to fit residues: 100.5945 Evaluate side-chains 302 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 262 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 365 optimal weight: 8.9990 chunk 362 optimal weight: 3.9990 chunk 360 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 347 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132443 restraints weight = 36098.960| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.04 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31866 Z= 0.129 Angle : 0.564 7.989 43482 Z= 0.299 Chirality : 0.042 0.209 4952 Planarity : 0.004 0.061 5309 Dihedral : 16.212 179.553 5261 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 16.98 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3661 helix: 1.76 (0.14), residues: 1477 sheet: -0.22 (0.25), residues: 426 loop : -1.53 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.014 0.001 TYR D 46 PHE 0.010 0.001 PHE C1144 TRP 0.017 0.001 TRP F 433 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (31858) covalent geometry : angle 0.56207 / 0.30 (43470) hydrogen bonds : bond 0.04826 / 3.40 ( 1358) hydrogen bonds : angle 4.29716 / 2.99 ( 3828) metal coordination : bond 0.00520 / 0.26 ( 8) metal coordination : angle 3.00437 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.289 Fit side-chains REVERT: B 170 ARG cc_start: 0.6612 (ttm110) cc_final: 0.6202 (ttm-80) REVERT: C 145 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 631 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: C 866 ASP cc_start: 0.8916 (p0) cc_final: 0.8637 (p0) REVERT: D 129 ASP cc_start: 0.6958 (t0) cc_final: 0.6706 (t0) REVERT: D 227 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 697 MET cc_start: 0.8720 (ttp) cc_final: 0.8415 (ttp) outliers start: 53 outliers final: 41 residues processed: 298 average time/residue: 0.2009 time to fit residues: 95.9749 Evaluate side-chains 289 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 147 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 4 optimal weight: 0.0030 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 299 optimal weight: 0.7980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136219 restraints weight = 36163.789| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.83 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31866 Z= 0.134 Angle : 0.565 9.577 43482 Z= 0.297 Chirality : 0.042 0.202 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.173 179.050 5261 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.69 % Allowed : 17.23 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3661 helix: 1.82 (0.14), residues: 1480 sheet: -0.17 (0.25), residues: 441 loop : -1.52 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 542 TYR 0.013 0.001 TYR D 631 PHE 0.011 0.001 PHE D1319 TRP 0.010 0.001 TRP F 433 HIS 0.004 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (31858) covalent geometry : angle 0.56268 / 0.30 (43470) hydrogen bonds : bond 0.04775 / 3.37 ( 1358) hydrogen bonds : angle 4.21465 / 2.93 ( 3828) metal coordination : bond 0.00546 / 0.27 ( 8) metal coordination : angle 2.95512 / 1.70 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 1.301 Fit side-chains REVERT: B 170 ARG cc_start: 0.6469 (ttm110) cc_final: 0.6121 (ttm-80) REVERT: C 145 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8585 (mm) REVERT: C 542 ARG cc_start: 0.6530 (mtt-85) cc_final: 0.6222 (mtt-85) REVERT: C 631 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7545 (pp20) REVERT: C 866 ASP cc_start: 0.8929 (p0) cc_final: 0.8628 (p0) REVERT: D 129 ASP cc_start: 0.6965 (t0) cc_final: 0.6705 (t0) REVERT: D 227 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7597 (t80) REVERT: D 697 MET cc_start: 0.8721 (ttp) cc_final: 0.8358 (ttp) REVERT: D 714 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (mt-10) outliers start: 53 outliers final: 42 residues processed: 300 average time/residue: 0.2001 time to fit residues: 96.9865 Evaluate side-chains 296 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 364 optimal weight: 8.9990 chunk 277 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 367 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 218 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132673 restraints weight = 36267.864| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.09 r_work: 0.2870 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31866 Z= 0.139 Angle : 0.567 9.170 43482 Z= 0.299 Chirality : 0.042 0.202 4952 Planarity : 0.004 0.060 5309 Dihedral : 16.166 178.800 5261 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.62 % Allowed : 17.30 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3661 helix: 1.81 (0.14), residues: 1480 sheet: -0.16 (0.25), residues: 441 loop : -1.53 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.013 0.001 TYR D 46 PHE 0.010 0.001 PHE D1274 TRP 0.009 0.001 TRP F 433 HIS 0.004 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31858) covalent geometry : angle 0.56485 / 0.30 (43470) hydrogen bonds : bond 0.04782 / 3.38 ( 1358) hydrogen bonds : angle 4.20452 / 2.92 ( 3828) metal coordination : bond 0.00554 / 0.28 ( 8) metal coordination : angle 2.94500 / 1.69 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7077.43 seconds wall clock time: 122 minutes 7.78 seconds (7327.78 seconds total)