Starting phenix.real_space_refine on Sat Mar 7 07:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vcf_31890/03_2026/7vcf_31890.map" } resolution = 2.5 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= 0.037 sd= 0.144 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: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 2 5.21 5 S 139 5.16 5 C 25298 2.51 5 N 6868 2.21 5 O 7286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39626 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 12577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1496, 12577 Classifications: {'peptide': 1496} Link IDs: {'PTRANS': 57, 'TRANS': 1438} Chain breaks: 14 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5142 Classifications: {'peptide': 651} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 619} Chain breaks: 1 Chain: "C" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1728 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "F" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3139 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 378} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 612 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 861 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2751 Classifications: {'peptide': 363} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain: "K" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 939 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 105} Chain: "N" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 155 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "O" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1572 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain: "Q" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1244 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 14, 'TRANS': 134} Chain: "T" Number of atoms: 6185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6185 Classifications: {'peptide': 763} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 716} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'TPO:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "W" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1398 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 10, 'TRANS': 153} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 241 Unusual residues: {'IHP': 1, 'LMG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21375 SG CYS F 704 42.771 118.321 45.317 1.00 46.03 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 IHP A2005 " occ=0.50 ... (34 atoms not shown) pdb=" P6 IHP A2005 " occ=0.50 Time building chain proxies: 7.71, per 1000 atoms: 0.19 Number of scatterers: 39626 At special positions: 0 Unit cell: (129.353, 178.268, 227.183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 139 16.00 P 33 15.00 Mg 2 11.99 O 7286 8.00 N 6868 7.00 C 25298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 376 " - pdb=" SG CYS T 720 " distance=2.04 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: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9038 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 26 sheets defined 47.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 34 through 55 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.721A pdb=" N PHE A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.644A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 166 removed outlier: 3.523A pdb=" N GLY A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Proline residue: A 173 - end of helix removed outlier: 3.683A pdb=" N LEU A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 205 through 221 removed outlier: 3.815A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 250 through 282 removed outlier: 3.851A pdb=" N ASN A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.257A pdb=" N SER A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 322 Processing helix chain 'A' and resid 328 through 338 removed outlier: 4.221A pdb=" N ASN A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.801A pdb=" N THR A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.817A pdb=" N ILE A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 377' Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.543A pdb=" N GLN A 389 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.641A pdb=" N ARG A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.857A pdb=" N ASN A 430 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.721A pdb=" N THR A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.511A pdb=" N ASN A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 698 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 731 through 739 removed outlier: 3.625A pdb=" N TYR A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 834 removed outlier: 3.831A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 860 through 880 Processing helix chain 'A' and resid 881 through 887 removed outlier: 6.797A pdb=" N TYR A 884 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 885 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 897 removed outlier: 3.739A pdb=" N THR A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.578A pdb=" N ASN A 905 " --> pdb=" O SER A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 954 through 959 removed outlier: 4.078A pdb=" N THR A 959 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 Processing helix chain 'A' and resid 1046 through 1063 removed outlier: 3.801A pdb=" N GLU A1050 " --> pdb=" O PHE A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1104 removed outlier: 4.407A pdb=" N LYS A1079 " --> pdb=" O HIS A1075 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1143 Processing helix chain 'A' and resid 1155 through 1181 removed outlier: 3.638A pdb=" N LEU A1159 " --> pdb=" O THR A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1245 removed outlier: 3.579A pdb=" N TRP A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1262 removed outlier: 4.487A pdb=" N LYS A1255 " --> pdb=" O ARG A1251 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A1262 " --> pdb=" O ILE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1412 removed outlier: 3.785A pdb=" N GLN A1402 " --> pdb=" O LYS A1398 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN A1410 " --> pdb=" O ASN A1406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1436 Processing helix chain 'A' and resid 1438 through 1448 removed outlier: 3.732A pdb=" N ARG A1442 " --> pdb=" O HIS A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1490 removed outlier: 5.230A pdb=" N LEU A1483 " --> pdb=" O TRP A1479 " (cutoff:3.500A) Proline residue: A1484 - end of helix Processing helix chain 'A' and resid 1624 through 1631 Processing helix chain 'A' and resid 1640 through 1644 Processing helix chain 'A' and resid 1646 through 1654 Processing helix chain 'A' and resid 1690 through 1694 removed outlier: 3.684A pdb=" N LEU A1694 " --> pdb=" O LEU A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1719 removed outlier: 3.672A pdb=" N LYS A1703 " --> pdb=" O SER A1699 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A1704 " --> pdb=" O SER A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1725 Processing helix chain 'A' and resid 1745 through 1753 removed outlier: 4.147A pdb=" N ILE A1749 " --> pdb=" O SER A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1762 Processing helix chain 'A' and resid 1773 through 1787 Processing helix chain 'A' and resid 1803 through 1807 removed outlier: 3.577A pdb=" N TYR A1806 " --> pdb=" O ARG A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1971 Processing helix chain 'A' and resid 1973 through 1975 No H-bonds generated for 'chain 'A' and resid 1973 through 1975' Processing helix chain 'A' and resid 1976 through 1989 removed outlier: 3.611A pdb=" N GLN A1989 " --> pdb=" O LYS A1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.594A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.880A pdb=" N VAL B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.681A pdb=" N ASP B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.764A pdb=" N ILE B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.806A pdb=" N LEU B 440 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 663 Processing helix chain 'B' and resid 685 through 689 removed outlier: 3.807A pdb=" N TYR B 689 " --> pdb=" O ALA B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 727 Processing helix chain 'B' and resid 751 through 756 Processing helix chain 'C' and resid 257 through 277 Proline residue: C 262 - end of helix Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 288 removed outlier: 3.613A pdb=" N ARG C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 removed outlier: 3.813A pdb=" N TYR C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 327 through 364 removed outlier: 3.642A pdb=" N ILE C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 Processing helix chain 'C' and resid 379 through 387 Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 414 through 426 removed outlier: 4.018A pdb=" N GLU C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.756A pdb=" N ALA C 447 " --> pdb=" O GLY C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.610A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.647A pdb=" N ASP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 82 removed outlier: 3.645A pdb=" N ARG D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 541 removed outlier: 3.792A pdb=" N PHE F 536 " --> pdb=" O PRO F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 587 removed outlier: 3.662A pdb=" N VAL F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 578 " --> pdb=" O HIS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 624 removed outlier: 3.611A pdb=" N GLU F 594 " --> pdb=" O TRP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 650 removed outlier: 3.519A pdb=" N HIS F 650 " --> pdb=" O SER F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 909 removed outlier: 3.700A pdb=" N TRP F 908 " --> pdb=" O ARG F 905 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU F 909 " --> pdb=" O LEU F 906 " (cutoff:3.500A) Processing helix chain 'F' and resid 910 through 920 removed outlier: 3.831A pdb=" N ALA F 914 " --> pdb=" O LEU F 910 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 915 " --> pdb=" O LEU F 911 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN F 916 " --> pdb=" O LEU F 912 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE F 918 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 921 through 928 Processing helix chain 'G' and resid 329 through 374 removed outlier: 5.400A pdb=" N HIS G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) Proline residue: G 347 - end of helix removed outlier: 3.658A pdb=" N LEU G 374 " --> pdb=" O GLN G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 394 Processing helix chain 'H' and resid 75 through 105 Processing helix chain 'H' and resid 113 through 131 Proline residue: H 125 - end of helix removed outlier: 3.579A pdb=" N TYR H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 160 removed outlier: 3.734A pdb=" N PHE H 147 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 160 " --> pdb=" O VAL H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 29 Processing helix chain 'I' and resid 95 through 104 Processing helix chain 'I' and resid 223 through 238 Processing helix chain 'I' and resid 239 through 242 removed outlier: 3.572A pdb=" N ILE I 242 " --> pdb=" O GLU I 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 239 through 242' Processing helix chain 'I' and resid 243 through 249 removed outlier: 3.624A pdb=" N VAL I 249 " --> pdb=" O VAL I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.906A pdb=" N VAL K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER K 41 " --> pdb=" O PHE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 55 removed outlier: 3.986A pdb=" N GLN K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'M' and resid 24 through 44 removed outlier: 3.883A pdb=" N PHE M 28 " --> pdb=" O SER M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 78 Processing helix chain 'M' and resid 97 through 102 Processing helix chain 'M' and resid 102 through 111 removed outlier: 3.763A pdb=" N TRP M 111 " --> pdb=" O HIS M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 117 Processing helix chain 'N' and resid 1275 through 1288 removed outlier: 3.637A pdb=" N TYR N1280 " --> pdb=" O ALA N1276 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA N1281 " --> pdb=" O ALA N1277 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR N1287 " --> pdb=" O LEU N1283 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU N1288 " --> pdb=" O TYR N1284 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 168 Processing helix chain 'O' and resid 168 through 181 removed outlier: 3.544A pdb=" N PHE O 172 " --> pdb=" O SER O 168 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 206 removed outlier: 4.127A pdb=" N ALA O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY O 188 " --> pdb=" O PRO O 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 219 Processing helix chain 'O' and resid 224 through 231 Processing helix chain 'O' and resid 233 through 237 removed outlier: 3.611A pdb=" N ALA O 237 " --> pdb=" O ALA O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 261 Processing helix chain 'O' and resid 278 through 287 Processing helix chain 'O' and resid 288 through 303 removed outlier: 3.998A pdb=" N ALA O 292 " --> pdb=" O ASP O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 311 Processing helix chain 'O' and resid 314 through 323 Processing helix chain 'Q' and resid 80 through 93 removed outlier: 3.639A pdb=" N THR Q 93 " --> pdb=" O MET Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 106 removed outlier: 4.217A pdb=" N ASN Q 105 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA Q 106 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 140 Processing helix chain 'Q' and resid 159 through 169 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 194 through 200 Processing helix chain 'Q' and resid 201 through 215 Processing helix chain 'Q' and resid 215 through 227 removed outlier: 3.562A pdb=" N SER Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 19 removed outlier: 3.586A pdb=" N LYS T 18 " --> pdb=" O ASP T 15 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU T 19 " --> pdb=" O PRO T 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 15 through 19' Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 40 through 44 removed outlier: 3.541A pdb=" N ALA T 44 " --> pdb=" O GLU T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 67 removed outlier: 3.665A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 removed outlier: 3.691A pdb=" N MET T 80 " --> pdb=" O ASN T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 155 through 162 Processing helix chain 'T' and resid 172 through 186 removed outlier: 3.787A pdb=" N TYR T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 205 through 209 Processing helix chain 'T' and resid 214 through 221 Processing helix chain 'T' and resid 228 through 236 Processing helix chain 'T' and resid 271 through 277 Processing helix chain 'T' and resid 382 through 391 removed outlier: 3.507A pdb=" N ARG T 391 " --> pdb=" O TYR T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 394 through 409 removed outlier: 5.754A pdb=" N GLY T 404 " --> pdb=" O ARG T 400 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA T 405 " --> pdb=" O ARG T 401 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN T 409 " --> pdb=" O ALA T 405 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 427 No H-bonds generated for 'chain 'T' and resid 425 through 427' Processing helix chain 'T' and resid 428 through 438 Processing helix chain 'T' and resid 441 through 461 removed outlier: 3.503A pdb=" N ILE T 445 " --> pdb=" O ASP T 441 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA T 461 " --> pdb=" O ARG T 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 463 through 481 removed outlier: 3.712A pdb=" N ARG T 481 " --> pdb=" O GLU T 477 " (cutoff:3.500A) Processing helix chain 'T' and resid 515 through 520 Processing helix chain 'T' and resid 546 through 570 Processing helix chain 'T' and resid 582 through 587 Processing helix chain 'T' and resid 589 through 602 removed outlier: 3.543A pdb=" N ALA T 602 " --> pdb=" O SER T 598 " (cutoff:3.500A) Processing helix chain 'T' and resid 603 through 614 Processing helix chain 'T' and resid 643 through 658 removed outlier: 3.663A pdb=" N GLU T 656 " --> pdb=" O ALA T 652 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN T 657 " --> pdb=" O ARG T 653 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA T 658 " --> pdb=" O LEU T 654 " (cutoff:3.500A) Processing helix chain 'T' and resid 661 through 675 removed outlier: 3.676A pdb=" N TRP T 675 " --> pdb=" O LEU T 671 " (cutoff:3.500A) Processing helix chain 'T' and resid 721 through 741 Processing helix chain 'T' and resid 748 through 755 removed outlier: 3.674A pdb=" N ALA T 755 " --> pdb=" O GLY T 751 " (cutoff:3.500A) Processing helix chain 'T' and resid 776 through 780 Processing helix chain 'T' and resid 782 through 787 removed outlier: 3.804A pdb=" N LEU T 786 " --> pdb=" O GLY T 782 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS T 787 " --> pdb=" O PRO T 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 782 through 787' Processing helix chain 'T' and resid 793 through 813 removed outlier: 3.950A pdb=" N MET T 813 " --> pdb=" O ALA T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 824 through 856 Processing helix chain 'W' and resid 102 through 121 Proline residue: W 116 - end of helix Processing helix chain 'W' and resid 124 through 129 Processing helix chain 'W' and resid 131 through 139 removed outlier: 4.856A pdb=" N TRP W 136 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 148 Processing helix chain 'W' and resid 153 through 166 Processing helix chain 'W' and resid 173 through 198 Processing helix chain 'W' and resid 201 through 206 removed outlier: 3.540A pdb=" N TRP W 206 " --> pdb=" O THR W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 235 Processing helix chain 'W' and resid 243 through 257 removed outlier: 4.065A pdb=" N GLN W 256 " --> pdb=" O GLU W 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 removed outlier: 3.786A pdb=" N LEU I 187 " --> pdb=" O ASN I 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AA5, first strand: chain 'A' and resid 914 through 915 Processing sheet with id=AA6, first strand: chain 'A' and resid 941 through 942 removed outlier: 6.763A pdb=" N LEU A 941 " --> pdb=" O PHE T 816 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1348 through 1352 Processing sheet with id=AA8, first strand: chain 'A' and resid 1375 through 1376 removed outlier: 3.621A pdb=" N THR A1383 " --> pdb=" O THR A1389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1605 through 1606 Processing sheet with id=AB1, first strand: chain 'A' and resid 1638 through 1639 Processing sheet with id=AB2, first strand: chain 'A' and resid 1795 through 1796 Processing sheet with id=AB3, first strand: chain 'A' and resid 1826 through 1827 removed outlier: 3.880A pdb=" N VAL T 101 " --> pdb=" O THR A1827 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1922 through 1923 Processing sheet with id=AB5, first strand: chain 'B' and resid 163 through 169 removed outlier: 6.604A pdb=" N GLN B 232 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU B 165 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 253 removed outlier: 6.379A pdb=" N ARG B 315 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE B 306 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B 317 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 removed outlier: 5.683A pdb=" N ILE B 404 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 325 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU B 412 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 389 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 426 through 427 removed outlier: 6.112A pdb=" N GLU B 458 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N PHE B 478 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN B 499 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 480 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 486 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR B 491 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N GLN B 605 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU B 649 " --> pdb=" O GLN B 605 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR B 637 " --> pdb=" O GLY B 617 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 765 " --> pdb=" O ARG B 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 426 through 427 removed outlier: 4.743A pdb=" N MET F 844 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU F 826 " --> pdb=" O ARG F 852 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL F 793 " --> pdb=" O ALA F 816 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR F 791 " --> pdb=" O GLN F 818 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 772 " --> pdb=" O GLN F 798 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR F 800 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS F 770 " --> pdb=" O THR F 800 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP F 750 " --> pdb=" O LEU F 744 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU F 744 " --> pdb=" O ASP F 750 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS F 733 " --> pdb=" O HIS F 724 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS F 707 " --> pdb=" O ASN F 678 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ASN F 678 " --> pdb=" O LYS F 707 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 690 through 692 removed outlier: 3.745A pdb=" N LEU B 692 " --> pdb=" O GLY B 707 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 707 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 36 through 51 removed outlier: 3.727A pdb=" N GLY I 36 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY I 60 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE I 63 " --> pdb=" O HIS I 90 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N HIS I 90 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY I 65 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR I 88 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA I 67 " --> pdb=" O ASN I 86 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR I 113 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR I 128 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA I 115 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL I 126 " --> pdb=" O ALA I 115 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN I 117 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE I 124 " --> pdb=" O GLN I 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA I 334 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG I 349 " --> pdb=" O ALA I 334 " (cutoff:3.500A) removed outlier: 12.805A pdb=" N GLY I 348 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N VAL I 51 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN I 49 " --> pdb=" O PRO I 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 22 through 23 Processing sheet with id=AC4, first strand: chain 'Q' and resid 123 through 124 Processing sheet with id=AC5, first strand: chain 'Q' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'T' and resid 292 through 297 removed outlier: 6.738A pdb=" N THR T 303 " --> pdb=" O VAL T 318 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL T 318 " --> pdb=" O THR T 303 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU T 305 " --> pdb=" O MET T 316 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET T 316 " --> pdb=" O GLU T 305 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU T 307 " --> pdb=" O HIS T 314 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU T 352 " --> pdb=" O GLU T 343 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN T 345 " --> pdb=" O HIS T 350 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS T 350 " --> pdb=" O GLN T 345 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS T 376 " --> pdb=" O GLU T 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 491 through 493 Processing sheet with id=AC8, first strand: chain 'T' and resid 573 through 575 removed outlier: 6.828A pdb=" N LEU T 580 " --> pdb=" O ILE T 574 " (cutoff:3.500A) 1975 hydrogen bonds defined for protein. 5640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.68 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9587 1.33 - 1.45: 9377 1.45 - 1.58: 21290 1.58 - 1.70: 97 1.70 - 1.83: 245 Bond restraints: 40596 Sorted by residual: bond pdb=" OG1 TPO H 177 " pdb=" P TPO H 177 " ideal model delta sigma weight residual 1.717 1.578 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" OG1 TPO H 176 " pdb=" P TPO H 176 " ideal model delta sigma weight residual 1.717 1.583 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" OG1 TPO H 178 " pdb=" P TPO H 178 " ideal model delta sigma weight residual 1.717 1.587 0.130 2.00e-02 2.50e+03 4.19e+01 bond pdb=" OG1 TPO T 249 " pdb=" P TPO T 249 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" OG1 TPO T 77 " pdb=" P TPO T 77 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 40591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 53376 2.79 - 5.58: 1244 5.58 - 8.36: 239 8.36 - 11.15: 67 11.15 - 13.94: 12 Bond angle restraints: 54938 Sorted by residual: angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" C ASN A 282 " ideal model delta sigma weight residual 109.81 123.75 -13.94 2.21e+00 2.05e-01 3.98e+01 angle pdb=" C PRO T 544 " pdb=" N ARG T 545 " pdb=" CA ARG T 545 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N VAL A1790 " pdb=" CA VAL A1790 " pdb=" C VAL A1790 " ideal model delta sigma weight residual 111.44 103.77 7.67 1.34e+00 5.57e-01 3.28e+01 angle pdb=" N GLY F 695 " pdb=" CA GLY F 695 " pdb=" C GLY F 695 " ideal model delta sigma weight residual 112.51 120.91 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C GLY B 534 " pdb=" N GLN B 535 " pdb=" CA GLN B 535 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 ... (remaining 54933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.64: 23555 30.64 - 61.29: 704 61.29 - 91.93: 85 91.93 - 122.58: 15 122.58 - 153.22: 2 Dihedral angle restraints: 24361 sinusoidal: 10301 harmonic: 14060 Sorted by residual: dihedral pdb=" CA ASP A1252 " pdb=" C ASP A1252 " pdb=" N ARG A1253 " pdb=" CA ARG A1253 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C ASN A 282 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" CA TYR A 417 " pdb=" C TYR A 417 " pdb=" N GLY A 418 " pdb=" CA GLY A 418 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 24358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.925: 5788 0.925 - 1.849: 0 1.849 - 2.774: 0 2.774 - 3.698: 0 3.698 - 4.623: 4 Chirality restraints: 5792 Sorted by residual: chirality pdb=" C5 IHP A2005 " pdb=" C4 IHP A2005 " pdb=" C6 IHP A2005 " pdb=" O15 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.42 2.21 -4.62 2.00e-01 2.50e+01 5.34e+02 chirality pdb=" C2 IHP A2005 " pdb=" C1 IHP A2005 " pdb=" C3 IHP A2005 " pdb=" O12 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.52 2.10 -4.62 2.00e-01 2.50e+01 5.33e+02 chirality pdb=" C3 IHP A2005 " pdb=" C2 IHP A2005 " pdb=" C4 IHP A2005 " pdb=" O13 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.34 2.09 -4.42 2.00e-01 2.50e+01 4.89e+02 ... (remaining 5789 not shown) Planarity restraints: 7040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 LMG A2004 " -0.119 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C29 LMG A2004 " 0.036 2.00e-02 2.50e+03 pdb=" O10 LMG A2004 " 0.046 2.00e-02 2.50e+03 pdb=" O8 LMG A2004 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 LMG A2001 " 0.113 2.00e-02 2.50e+03 6.56e-02 4.30e+01 pdb=" C29 LMG A2001 " -0.034 2.00e-02 2.50e+03 pdb=" O10 LMG A2001 " -0.044 2.00e-02 2.50e+03 pdb=" O8 LMG A2001 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 550 " 0.012 2.00e-02 2.50e+03 3.47e-02 3.01e+01 pdb=" CG TRP F 550 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP F 550 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP F 550 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 550 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP F 550 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP F 550 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 550 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 550 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 550 " -0.001 2.00e-02 2.50e+03 ... (remaining 7037 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 307 2.63 - 3.19: 31363 3.19 - 3.76: 59452 3.76 - 4.33: 83457 4.33 - 4.90: 138039 Nonbonded interactions: 312618 Sorted by model distance: nonbonded pdb=" O3P TPO T 712 " pdb="MG MG T1001 " model vdw 2.057 2.170 nonbonded pdb=" O THR A1228 " pdb=" OD1 ASP A1229 " model vdw 2.127 3.040 nonbonded pdb=" O PHE H 149 " pdb=" NE2 GLN H 153 " model vdw 2.195 3.120 nonbonded pdb=" ND1 HIS T 374 " pdb=" O TYR T 416 " model vdw 2.209 3.120 nonbonded pdb=" O2P TPO T 712 " pdb="MG MG T1001 " model vdw 2.214 2.170 ... (remaining 312613 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 3.540 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.710 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.007 0.139 40597 Z= 0.346 Angle : 1.084 13.941 54940 Z= 0.571 Chirality : 0.133 4.623 5792 Planarity : 0.009 0.109 7040 Dihedral : 15.162 153.220 15320 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 0.19 % Allowed : 0.46 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.21 (0.11), residues: 4699 helix: -0.38 (0.10), residues: 2013 sheet: 0.46 (0.20), residues: 629 loop : -1.59 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 136 TYR 0.049 0.003 TYR A1721 PHE 0.044 0.003 PHE A 44 TRP 0.082 0.003 TRP F 550 HIS 0.027 0.002 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00727 (40596) covalent geometry : angle 1.08365 (54938) SS BOND : bond 0.00570 ( 1) SS BOND : angle 3.24748 ( 2) hydrogen bonds : bond 0.15412 ( 1973) hydrogen bonds : angle 6.17983 ( 5640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 466 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1402 GLN cc_start: 0.7619 (mm110) cc_final: 0.7353 (mp10) REVERT: A 1891 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6444 (tpt170) REVERT: B 257 MET cc_start: 0.8076 (ttt) cc_final: 0.7594 (ttt) REVERT: C 276 LEU cc_start: 0.8761 (tt) cc_final: 0.8337 (tp) REVERT: G 378 ARG cc_start: 0.7179 (mmp80) cc_final: 0.6797 (mmp-170) REVERT: H 100 ARG cc_start: 0.6882 (mmm-85) cc_final: 0.6590 (tpt90) REVERT: O 143 LYS cc_start: 0.7470 (tptt) cc_final: 0.7126 (tptp) REVERT: T 378 MET cc_start: 0.8320 (ttm) cc_final: 0.8101 (ttm) outliers start: 8 outliers final: 3 residues processed: 472 average time/residue: 0.9242 time to fit residues: 512.9182 Evaluate side-chains 368 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 364 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain W residue 256 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 431 HIS A 822 HIS A 838 ASN A1075 HIS A1609 ASN A1702 GLN B 703 HIS C 453 GLN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 733 HIS F 867 ASN I 264 ASN K 84 ASN W 256 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104804 restraints weight = 64739.715| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40597 Z= 0.159 Angle : 0.669 15.254 54940 Z= 0.345 Chirality : 0.044 0.295 5792 Planarity : 0.006 0.073 7040 Dihedral : 9.597 115.001 5718 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.14 % Allowed : 6.77 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.12), residues: 4699 helix: 1.00 (0.11), residues: 2022 sheet: 0.64 (0.20), residues: 631 loop : -1.38 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 545 TYR 0.016 0.002 TYR A 726 PHE 0.042 0.002 PHE H 87 TRP 0.026 0.002 TRP G 388 HIS 0.007 0.001 HIS A1444 Details of bonding type rmsd covalent geometry : bond 0.00348 (40596) covalent geometry : angle 0.66926 (54938) SS BOND : bond 0.00753 ( 1) SS BOND : angle 2.38002 ( 2) hydrogen bonds : bond 0.06186 ( 1973) hydrogen bonds : angle 4.89656 ( 5640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 403 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7858 (mp0) REVERT: A 210 TRP cc_start: 0.7679 (m100) cc_final: 0.7366 (m-90) REVERT: A 665 TYR cc_start: 0.6711 (m-10) cc_final: 0.6480 (m-10) REVERT: A 1402 GLN cc_start: 0.7362 (mm110) cc_final: 0.6994 (mp10) REVERT: A 1891 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6450 (tpt170) REVERT: B 257 MET cc_start: 0.7861 (ttt) cc_final: 0.7370 (ttt) REVERT: B 378 MET cc_start: 0.7488 (tpt) cc_final: 0.7178 (tpt) REVERT: B 421 ASP cc_start: 0.8325 (t0) cc_final: 0.8048 (t0) REVERT: B 796 GLU cc_start: 0.7953 (pt0) cc_final: 0.7173 (tp30) REVERT: C 276 LEU cc_start: 0.8606 (tt) cc_final: 0.8159 (tp) REVERT: F 615 GLU cc_start: 0.7133 (tp30) cc_final: 0.6814 (tp30) REVERT: G 357 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: G 378 ARG cc_start: 0.7500 (mmp80) cc_final: 0.6988 (mtp180) REVERT: H 100 ARG cc_start: 0.7116 (mmm-85) cc_final: 0.6448 (tpt90) REVERT: I 278 ASP cc_start: 0.7569 (p0) cc_final: 0.7347 (t0) REVERT: I 332 ARG cc_start: 0.5211 (ptp-110) cc_final: 0.4946 (ptp-110) REVERT: M 72 MET cc_start: 0.8808 (mtm) cc_final: 0.8464 (mtp) REVERT: O 146 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6314 (mpt180) REVERT: O 219 ASP cc_start: 0.6231 (m-30) cc_final: 0.5248 (p0) REVERT: T 267 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: T 498 ARG cc_start: 0.7378 (mmm160) cc_final: 0.7094 (mmm160) REVERT: T 784 LEU cc_start: 0.9279 (tt) cc_final: 0.9064 (tm) REVERT: W 96 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6477 (ttp-170) outliers start: 47 outliers final: 16 residues processed: 423 average time/residue: 0.8595 time to fit residues: 430.8516 Evaluate side-chains 386 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 366 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 256 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 28 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 446 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 461 optimal weight: 0.0670 chunk 158 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS B 703 HIS C 453 GLN F 573 ASN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 ASN K 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.135684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101477 restraints weight = 64740.568| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 40597 Z= 0.223 Angle : 0.710 12.254 54940 Z= 0.367 Chirality : 0.047 0.276 5792 Planarity : 0.006 0.074 7040 Dihedral : 8.998 104.204 5714 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 1.69 % Allowed : 9.28 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.12), residues: 4699 helix: 1.30 (0.11), residues: 2033 sheet: 0.64 (0.20), residues: 634 loop : -1.32 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1808 TYR 0.024 0.002 TYR A 86 PHE 0.030 0.002 PHE M 28 TRP 0.026 0.002 TRP G 388 HIS 0.012 0.002 HIS A1444 Details of bonding type rmsd covalent geometry : bond 0.00531 (40596) covalent geometry : angle 0.70952 (54938) SS BOND : bond 0.01155 ( 1) SS BOND : angle 2.63834 ( 2) hydrogen bonds : bond 0.07126 ( 1973) hydrogen bonds : angle 4.82619 ( 5640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 391 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 210 TRP cc_start: 0.7692 (m100) cc_final: 0.7421 (m-90) REVERT: A 1402 GLN cc_start: 0.7353 (mm110) cc_final: 0.6911 (mp10) REVERT: A 1476 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: A 1891 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6457 (tpt170) REVERT: B 421 ASP cc_start: 0.8239 (t0) cc_final: 0.7977 (t0) REVERT: B 796 GLU cc_start: 0.7991 (pt0) cc_final: 0.7297 (tp30) REVERT: C 276 LEU cc_start: 0.8696 (tt) cc_final: 0.8314 (tp) REVERT: F 615 GLU cc_start: 0.7167 (tp30) cc_final: 0.6887 (tp30) REVERT: G 360 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: H 100 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6482 (tpt90) REVERT: O 143 LYS cc_start: 0.7319 (tptp) cc_final: 0.6949 (tptp) REVERT: O 146 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6327 (mpt180) REVERT: O 219 ASP cc_start: 0.6162 (m-30) cc_final: 0.5289 (p0) REVERT: O 301 LYS cc_start: 0.7557 (tttt) cc_final: 0.7146 (ptmm) REVERT: Q 121 ARG cc_start: 0.7310 (ppp80) cc_final: 0.7070 (ptm160) REVERT: T 109 GLU cc_start: 0.7795 (mp0) cc_final: 0.7525 (pm20) REVERT: T 267 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: T 408 LYS cc_start: 0.8574 (mttp) cc_final: 0.8106 (mmmt) REVERT: T 719 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8084 (mtm) REVERT: T 784 LEU cc_start: 0.9282 (tt) cc_final: 0.9024 (tm) REVERT: T 798 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7699 (mm-40) REVERT: T 848 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6984 (mm) REVERT: W 96 ARG cc_start: 0.7163 (ttm-80) cc_final: 0.6714 (ttp-170) outliers start: 70 outliers final: 34 residues processed: 429 average time/residue: 0.8970 time to fit residues: 455.0583 Evaluate side-chains 409 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 368 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 382 optimal weight: 2.9990 chunk 413 optimal weight: 0.5980 chunk 469 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 317 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 463 optimal weight: 2.9990 chunk 257 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 453 GLN F 573 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 ASN Q 161 HIS T 771 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.138508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105371 restraints weight = 65227.085| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.87 r_work: 0.3217 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40597 Z= 0.110 Angle : 0.560 9.030 54940 Z= 0.290 Chirality : 0.041 0.257 5792 Planarity : 0.004 0.071 7040 Dihedral : 7.837 92.334 5711 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.60 % Allowed : 10.90 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.62 (0.12), residues: 4699 helix: 1.80 (0.12), residues: 2033 sheet: 0.71 (0.20), residues: 638 loop : -1.18 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 662 TYR 0.017 0.001 TYR A 304 PHE 0.027 0.001 PHE A 872 TRP 0.020 0.001 TRP G 388 HIS 0.003 0.001 HIS A1807 Details of bonding type rmsd covalent geometry : bond 0.00227 (40596) covalent geometry : angle 0.55981 (54938) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.44557 ( 2) hydrogen bonds : bond 0.04592 ( 1973) hydrogen bonds : angle 4.45716 ( 5640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 412 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7730 (t80) cc_final: 0.7228 (t80) REVERT: A 48 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 210 TRP cc_start: 0.7483 (m100) cc_final: 0.7238 (m-90) REVERT: A 1402 GLN cc_start: 0.7336 (mm110) cc_final: 0.6910 (mp10) REVERT: A 1891 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6457 (tpt170) REVERT: B 213 ASP cc_start: 0.7381 (p0) cc_final: 0.6702 (m-30) REVERT: B 421 ASP cc_start: 0.8131 (t0) cc_final: 0.7893 (OUTLIER) REVERT: B 796 GLU cc_start: 0.7926 (pt0) cc_final: 0.7347 (tp30) REVERT: F 561 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6706 (pt0) REVERT: F 588 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6862 (m-30) REVERT: F 677 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7524 (pp) REVERT: F 897 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7925 (t0) REVERT: G 357 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: H 100 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6397 (tpt90) REVERT: K 65 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7104 (mtm180) REVERT: M 72 MET cc_start: 0.8863 (mtm) cc_final: 0.8502 (mtp) REVERT: O 143 LYS cc_start: 0.7271 (tptp) cc_final: 0.6871 (tptp) REVERT: O 146 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6272 (mpt180) REVERT: O 175 THR cc_start: 0.8094 (m) cc_final: 0.7804 (m) REVERT: O 219 ASP cc_start: 0.5987 (m-30) cc_final: 0.5197 (p0) REVERT: T 109 GLU cc_start: 0.7727 (mp0) cc_final: 0.7502 (pm20) REVERT: T 408 LYS cc_start: 0.8448 (mttp) cc_final: 0.8093 (mmmt) REVERT: T 498 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7165 (mmm160) REVERT: T 719 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7733 (mtm) REVERT: T 784 LEU cc_start: 0.9296 (tt) cc_final: 0.9040 (tm) REVERT: T 848 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6883 (mm) REVERT: W 96 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6607 (ttp-170) REVERT: W 191 MET cc_start: 0.8912 (mtm) cc_final: 0.8703 (mtm) outliers start: 66 outliers final: 26 residues processed: 450 average time/residue: 0.8941 time to fit residues: 476.7557 Evaluate side-chains 412 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 377 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 801 LEU Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 108 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 312 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 446 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN A1702 GLN B 247 ASN C 453 GLN F 573 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 ASN K 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103792 restraints weight = 64673.588| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.03 r_work: 0.3159 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40597 Z= 0.154 Angle : 0.605 9.196 54940 Z= 0.313 Chirality : 0.043 0.284 5792 Planarity : 0.005 0.066 7040 Dihedral : 7.662 88.836 5711 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 1.91 % Allowed : 12.16 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.66 (0.12), residues: 4699 helix: 1.84 (0.12), residues: 2043 sheet: 0.72 (0.20), residues: 638 loop : -1.18 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 662 TYR 0.018 0.002 TYR A 304 PHE 0.032 0.002 PHE A 872 TRP 0.024 0.002 TRP G 388 HIS 0.007 0.001 HIS A1444 Details of bonding type rmsd covalent geometry : bond 0.00352 (40596) covalent geometry : angle 0.60528 (54938) SS BOND : bond 0.00879 ( 1) SS BOND : angle 1.83341 ( 2) hydrogen bonds : bond 0.05608 ( 1973) hydrogen bonds : angle 4.46917 ( 5640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 371 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: A 44 PHE cc_start: 0.7788 (t80) cc_final: 0.7254 (t80) REVERT: A 48 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 210 TRP cc_start: 0.7597 (m100) cc_final: 0.7364 (m-90) REVERT: A 1063 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 1402 GLN cc_start: 0.7390 (mm110) cc_final: 0.6929 (mp10) REVERT: A 1476 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: A 1891 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6469 (tpt170) REVERT: B 421 ASP cc_start: 0.8173 (t0) cc_final: 0.7937 (t0) REVERT: B 796 GLU cc_start: 0.7965 (pt0) cc_final: 0.7331 (tp30) REVERT: C 276 LEU cc_start: 0.8379 (tt) cc_final: 0.8160 (tp) REVERT: F 588 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: F 615 GLU cc_start: 0.7137 (tp30) cc_final: 0.6836 (tp30) REVERT: F 677 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7563 (pp) REVERT: F 897 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7908 (t0) REVERT: H 100 ARG cc_start: 0.6871 (mmm-85) cc_final: 0.6299 (tpt90) REVERT: H 159 MET cc_start: 0.0141 (OUTLIER) cc_final: -0.0109 (mmt) REVERT: K 65 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7072 (mtm180) REVERT: O 146 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6293 (mpt180) REVERT: O 175 THR cc_start: 0.8113 (m) cc_final: 0.7823 (m) REVERT: O 301 LYS cc_start: 0.7537 (tttt) cc_final: 0.7139 (ptmm) REVERT: T 109 GLU cc_start: 0.7795 (mp0) cc_final: 0.7543 (pm20) REVERT: T 408 LYS cc_start: 0.8479 (mttp) cc_final: 0.8079 (mmmt) REVERT: T 555 MET cc_start: 0.8822 (mtp) cc_final: 0.8562 (mtm) REVERT: T 719 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: T 798 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7568 (mm-40) REVERT: T 848 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6995 (mm) REVERT: W 96 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.6652 (ttp-170) REVERT: W 191 MET cc_start: 0.8984 (mtm) cc_final: 0.8774 (mtm) outliers start: 79 outliers final: 37 residues processed: 413 average time/residue: 0.8737 time to fit residues: 427.2077 Evaluate side-chains 413 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 195 PHE Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 442 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 325 optimal weight: 0.3980 chunk 256 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1609 ASN A1674 ASN C 453 GLN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 ASN K 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.136928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103668 restraints weight = 64596.959| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.13 r_work: 0.3150 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 40597 Z= 0.155 Angle : 0.606 9.655 54940 Z= 0.313 Chirality : 0.044 0.296 5792 Planarity : 0.005 0.066 7040 Dihedral : 7.545 87.292 5711 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.69 (0.12), residues: 4699 helix: 1.86 (0.12), residues: 2042 sheet: 0.76 (0.20), residues: 636 loop : -1.16 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 662 TYR 0.026 0.002 TYR A 86 PHE 0.031 0.002 PHE A 872 TRP 0.027 0.002 TRP A 278 HIS 0.007 0.001 HIS A1444 Details of bonding type rmsd covalent geometry : bond 0.00358 (40596) covalent geometry : angle 0.60563 (54938) SS BOND : bond 0.00808 ( 1) SS BOND : angle 1.92229 ( 2) hydrogen bonds : bond 0.05694 ( 1973) hydrogen bonds : angle 4.47220 ( 5640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 369 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: A 44 PHE cc_start: 0.7805 (t80) cc_final: 0.7261 (t80) REVERT: A 48 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 210 TRP cc_start: 0.7631 (m100) cc_final: 0.7394 (m-90) REVERT: A 1402 GLN cc_start: 0.7370 (mm110) cc_final: 0.6914 (mp10) REVERT: A 1476 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: A 1891 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6401 (tpm170) REVERT: B 213 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: B 421 ASP cc_start: 0.8181 (t0) cc_final: 0.7929 (OUTLIER) REVERT: B 458 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: B 796 GLU cc_start: 0.7956 (pt0) cc_final: 0.7305 (tp30) REVERT: C 276 LEU cc_start: 0.8430 (tt) cc_final: 0.8186 (tp) REVERT: F 588 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: F 615 GLU cc_start: 0.7158 (tp30) cc_final: 0.6859 (tp30) REVERT: F 677 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7552 (pp) REVERT: F 897 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7898 (OUTLIER) REVERT: H 100 ARG cc_start: 0.6761 (mmm-85) cc_final: 0.6172 (tpt90) REVERT: H 159 MET cc_start: 0.0157 (OUTLIER) cc_final: -0.0237 (mmt) REVERT: K 49 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6662 (mmm) REVERT: K 65 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7094 (mtm180) REVERT: O 146 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6330 (mpt180) REVERT: O 301 LYS cc_start: 0.7529 (tttt) cc_final: 0.7131 (ptmm) REVERT: T 109 GLU cc_start: 0.7736 (mp0) cc_final: 0.7503 (pm20) REVERT: T 408 LYS cc_start: 0.8552 (mttp) cc_final: 0.8122 (mmmt) REVERT: T 458 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8135 (tptp) REVERT: T 555 MET cc_start: 0.8758 (mtp) cc_final: 0.8475 (mtm) REVERT: T 719 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: T 798 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7386 (mm-40) REVERT: T 848 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6882 (mm) REVERT: W 96 ARG cc_start: 0.6950 (ttm-80) cc_final: 0.6638 (ttp-170) REVERT: W 191 MET cc_start: 0.8996 (mtm) cc_final: 0.8744 (mtm) outliers start: 86 outliers final: 45 residues processed: 417 average time/residue: 0.8614 time to fit residues: 425.5204 Evaluate side-chains 419 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 361 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 458 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 420 optimal weight: 0.6980 chunk 317 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 322 optimal weight: 0.0010 chunk 109 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 453 GLN D 41 GLN F 573 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.137061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103624 restraints weight = 64372.983| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.03 r_work: 0.3156 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40597 Z= 0.157 Angle : 0.612 15.890 54940 Z= 0.314 Chirality : 0.044 0.320 5792 Planarity : 0.005 0.066 7040 Dihedral : 7.477 86.664 5711 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.13 % Allowed : 12.86 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.71 (0.12), residues: 4699 helix: 1.89 (0.12), residues: 2036 sheet: 0.77 (0.20), residues: 636 loop : -1.15 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 662 TYR 0.016 0.001 TYR A 304 PHE 0.031 0.002 PHE A 872 TRP 0.028 0.002 TRP A 278 HIS 0.007 0.001 HIS A1075 Details of bonding type rmsd covalent geometry : bond 0.00362 (40596) covalent geometry : angle 0.61151 (54938) SS BOND : bond 0.00870 ( 1) SS BOND : angle 1.86100 ( 2) hydrogen bonds : bond 0.05720 ( 1973) hydrogen bonds : angle 4.46229 ( 5640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 370 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6779 (tp30) REVERT: A 44 PHE cc_start: 0.7813 (t80) cc_final: 0.7286 (t80) REVERT: A 48 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 210 TRP cc_start: 0.7683 (m100) cc_final: 0.7464 (m-90) REVERT: A 1402 GLN cc_start: 0.7416 (mm110) cc_final: 0.6970 (mp10) REVERT: A 1473 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: A 1476 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: A 1891 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6478 (tpm170) REVERT: B 213 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: B 378 MET cc_start: 0.7353 (tpt) cc_final: 0.7052 (tpt) REVERT: B 395 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 421 ASP cc_start: 0.8196 (t0) cc_final: 0.7953 (OUTLIER) REVERT: B 796 GLU cc_start: 0.7980 (pt0) cc_final: 0.7342 (tp30) REVERT: C 442 ARG cc_start: 0.7315 (ttt90) cc_final: 0.7023 (mmm-85) REVERT: F 588 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: F 615 GLU cc_start: 0.7165 (tp30) cc_final: 0.6862 (tp30) REVERT: F 677 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7628 (pp) REVERT: H 100 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6377 (tpt90) REVERT: H 159 MET cc_start: 0.0256 (OUTLIER) cc_final: 0.0024 (mmt) REVERT: K 65 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7111 (mtm180) REVERT: N 1283 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7532 (tm) REVERT: O 146 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6419 (mpt180) REVERT: O 301 LYS cc_start: 0.7544 (tttt) cc_final: 0.7137 (ptmm) REVERT: T 78 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: T 408 LYS cc_start: 0.8592 (mttp) cc_final: 0.8177 (mmmt) REVERT: T 719 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7827 (mtm) REVERT: T 798 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7507 (mm-40) REVERT: T 848 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6989 (mm) REVERT: W 96 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6735 (ttp-170) REVERT: W 191 MET cc_start: 0.8989 (mtm) cc_final: 0.8740 (mtm) outliers start: 88 outliers final: 48 residues processed: 417 average time/residue: 0.8282 time to fit residues: 410.5817 Evaluate side-chains 423 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 360 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1473 GLU Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 230 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 341 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 450 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 453 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104163 restraints weight = 64520.765| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.16 r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40597 Z= 0.138 Angle : 0.596 15.184 54940 Z= 0.305 Chirality : 0.043 0.288 5792 Planarity : 0.005 0.065 7040 Dihedral : 7.366 85.478 5711 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 1.84 % Allowed : 13.61 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.77 (0.12), residues: 4699 helix: 1.94 (0.12), residues: 2043 sheet: 0.81 (0.20), residues: 636 loop : -1.13 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 662 TYR 0.015 0.001 TYR A 304 PHE 0.032 0.001 PHE A 872 TRP 0.030 0.001 TRP A 278 HIS 0.005 0.001 HIS A1747 Details of bonding type rmsd covalent geometry : bond 0.00310 (40596) covalent geometry : angle 0.59567 (54938) SS BOND : bond 0.00714 ( 1) SS BOND : angle 1.64211 ( 2) hydrogen bonds : bond 0.05346 ( 1973) hydrogen bonds : angle 4.39911 ( 5640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7770 (t80) cc_final: 0.7271 (t80) REVERT: A 48 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 210 TRP cc_start: 0.7674 (m100) cc_final: 0.7446 (m-90) REVERT: A 1402 GLN cc_start: 0.7362 (mm110) cc_final: 0.6918 (mp10) REVERT: A 1476 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: A 1891 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6570 (tpm170) REVERT: B 213 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: B 378 MET cc_start: 0.7324 (tpt) cc_final: 0.7022 (tpt) REVERT: B 395 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: B 421 ASP cc_start: 0.8173 (t0) cc_final: 0.7860 (t0) REVERT: B 796 GLU cc_start: 0.7949 (pt0) cc_final: 0.7291 (tp30) REVERT: C 442 ARG cc_start: 0.7236 (ttt90) cc_final: 0.6996 (ttm-80) REVERT: F 588 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: F 615 GLU cc_start: 0.7148 (tp30) cc_final: 0.6843 (tp30) REVERT: F 677 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7533 (pp) REVERT: H 100 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6307 (tpt90) REVERT: H 159 MET cc_start: 0.0226 (OUTLIER) cc_final: -0.0017 (mmt) REVERT: K 65 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7095 (mtm180) REVERT: N 1283 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7499 (tm) REVERT: O 146 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6371 (mpt180) REVERT: O 175 THR cc_start: 0.8126 (m) cc_final: 0.7848 (m) REVERT: O 301 LYS cc_start: 0.7484 (tttt) cc_final: 0.7053 (ptmm) REVERT: T 408 LYS cc_start: 0.8559 (mttp) cc_final: 0.8130 (mmmt) REVERT: T 458 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8056 (tptp) REVERT: T 719 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: T 798 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7361 (mm-40) REVERT: T 848 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6850 (mm) REVERT: W 96 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6714 (ttp-170) REVERT: W 191 MET cc_start: 0.8977 (mtm) cc_final: 0.8721 (mtm) outliers start: 76 outliers final: 41 residues processed: 416 average time/residue: 0.8513 time to fit residues: 419.4867 Evaluate side-chains 418 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 458 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 226 optimal weight: 2.9990 chunk 289 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 387 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 380 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 315 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 604 ASN C 453 GLN D 41 GLN F 573 ASN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102561 restraints weight = 64519.129| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.03 r_work: 0.3131 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 40597 Z= 0.205 Angle : 0.667 14.917 54940 Z= 0.343 Chirality : 0.046 0.377 5792 Planarity : 0.005 0.069 7040 Dihedral : 7.558 87.208 5711 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 1.84 % Allowed : 14.02 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.64 (0.12), residues: 4699 helix: 1.80 (0.12), residues: 2030 sheet: 0.79 (0.20), residues: 636 loop : -1.16 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 662 TYR 0.019 0.002 TYR A 728 PHE 0.033 0.002 PHE A 872 TRP 0.033 0.002 TRP A 278 HIS 0.010 0.002 HIS A1075 Details of bonding type rmsd covalent geometry : bond 0.00490 (40596) covalent geometry : angle 0.66716 (54938) SS BOND : bond 0.01082 ( 1) SS BOND : angle 2.20093 ( 2) hydrogen bonds : bond 0.06517 ( 1973) hydrogen bonds : angle 4.53706 ( 5640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: A 210 TRP cc_start: 0.7676 (m100) cc_final: 0.7448 (m-90) REVERT: A 1402 GLN cc_start: 0.7331 (mm110) cc_final: 0.6860 (mp10) REVERT: A 1476 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: A 1891 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6680 (tpm170) REVERT: B 213 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: B 378 MET cc_start: 0.7316 (tpt) cc_final: 0.7032 (tpt) REVERT: B 395 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 421 ASP cc_start: 0.8179 (t0) cc_final: 0.7836 (t0) REVERT: B 796 GLU cc_start: 0.8058 (pt0) cc_final: 0.7339 (tp30) REVERT: C 442 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6981 (ttm-80) REVERT: F 615 GLU cc_start: 0.7123 (tp30) cc_final: 0.6825 (tp30) REVERT: H 99 MET cc_start: 0.6941 (mmm) cc_final: 0.6677 (mmm) REVERT: H 100 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6332 (tpt90) REVERT: H 159 MET cc_start: 0.0379 (OUTLIER) cc_final: 0.0083 (mmt) REVERT: K 65 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7114 (mtm180) REVERT: N 1283 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7571 (tm) REVERT: O 146 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6373 (mpt180) REVERT: O 219 ASP cc_start: 0.6254 (m-30) cc_final: 0.5429 (p0) REVERT: O 301 LYS cc_start: 0.7597 (tttt) cc_final: 0.7194 (ptmm) REVERT: T 245 ASP cc_start: 0.8461 (t70) cc_final: 0.8197 (OUTLIER) REVERT: T 408 LYS cc_start: 0.8639 (mttp) cc_final: 0.8187 (mmmt) REVERT: T 458 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8076 (tptp) REVERT: T 719 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: T 798 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7566 (mm-40) REVERT: W 96 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6775 (ttp-170) outliers start: 76 outliers final: 50 residues processed: 415 average time/residue: 0.8447 time to fit residues: 415.2138 Evaluate side-chains 426 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 366 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 645 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 419 ASN Chi-restraints excluded: chain T residue 458 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 94 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 370 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 363 optimal weight: 0.0570 chunk 419 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN C 453 GLN D 41 GLN D 60 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104812 restraints weight = 64367.681| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.00 r_work: 0.3178 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40597 Z= 0.129 Angle : 0.595 14.956 54940 Z= 0.304 Chirality : 0.043 0.319 5792 Planarity : 0.005 0.066 7040 Dihedral : 7.303 84.576 5711 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 1.52 % Allowed : 14.41 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.12), residues: 4699 helix: 1.94 (0.12), residues: 2046 sheet: 0.82 (0.20), residues: 635 loop : -1.12 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 662 TYR 0.015 0.001 TYR A 304 PHE 0.034 0.001 PHE A 872 TRP 0.034 0.001 TRP A 278 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00285 (40596) covalent geometry : angle 0.59478 (54938) SS BOND : bond 0.00640 ( 1) SS BOND : angle 1.52409 ( 2) hydrogen bonds : bond 0.05130 ( 1973) hydrogen bonds : angle 4.36876 ( 5640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 375 time to evaluate : 1.351 Fit side-chains REVERT: A 44 PHE cc_start: 0.7731 (t80) cc_final: 0.7436 (t80) REVERT: A 210 TRP cc_start: 0.7625 (m100) cc_final: 0.7394 (m-90) REVERT: A 1402 GLN cc_start: 0.7384 (mm110) cc_final: 0.6939 (mp10) REVERT: A 1476 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: A 1891 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6441 (tpm170) REVERT: B 213 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: B 378 MET cc_start: 0.7387 (tpt) cc_final: 0.7032 (tpt) REVERT: B 421 ASP cc_start: 0.8215 (t0) cc_final: 0.7932 (t0) REVERT: B 796 GLU cc_start: 0.7911 (pt0) cc_final: 0.7301 (tp30) REVERT: C 442 ARG cc_start: 0.7329 (ttt90) cc_final: 0.7118 (ttm-80) REVERT: F 588 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: F 615 GLU cc_start: 0.7164 (tp30) cc_final: 0.6858 (tp30) REVERT: F 677 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7523 (pp) REVERT: G 378 ARG cc_start: 0.7476 (mmp80) cc_final: 0.6996 (mtp180) REVERT: H 99 MET cc_start: 0.7038 (mmm) cc_final: 0.6765 (mmm) REVERT: H 159 MET cc_start: 0.0556 (OUTLIER) cc_final: 0.0205 (mmt) REVERT: K 65 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7087 (mtm180) REVERT: N 1283 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7524 (tm) REVERT: O 146 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6415 (mpt180) REVERT: O 175 THR cc_start: 0.8184 (m) cc_final: 0.7907 (m) REVERT: O 204 ARG cc_start: 0.5673 (mtm-85) cc_final: 0.5448 (mtm-85) REVERT: O 219 ASP cc_start: 0.6178 (m-30) cc_final: 0.5388 (p0) REVERT: T 408 LYS cc_start: 0.8521 (mttp) cc_final: 0.8131 (mmmt) REVERT: T 458 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8106 (tptp) REVERT: T 555 MET cc_start: 0.8769 (mtp) cc_final: 0.8540 (mtm) REVERT: T 719 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: T 798 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7357 (mm-40) REVERT: T 848 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7155 (mm) REVERT: W 96 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.6817 (ttp-170) outliers start: 63 outliers final: 41 residues processed: 408 average time/residue: 0.8327 time to fit residues: 403.2482 Evaluate side-chains 422 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1353 SER Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 458 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 406 optimal weight: 7.9990 chunk 138 optimal weight: 0.0770 chunk 283 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 437 optimal weight: 3.9990 chunk 419 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1609 ASN C 453 GLN D 41 GLN F 573 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 ASN W 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102674 restraints weight = 64702.078| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.09 r_work: 0.3161 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40597 Z= 0.152 Angle : 0.613 14.906 54940 Z= 0.315 Chirality : 0.044 0.321 5792 Planarity : 0.005 0.067 7040 Dihedral : 7.321 86.125 5711 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 1.62 % Allowed : 14.29 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.12), residues: 4699 helix: 1.94 (0.12), residues: 2042 sheet: 0.80 (0.20), residues: 636 loop : -1.12 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 662 TYR 0.017 0.001 TYR N1287 PHE 0.034 0.002 PHE A 872 TRP 0.033 0.002 TRP A 278 HIS 0.006 0.001 HIS A1075 Details of bonding type rmsd covalent geometry : bond 0.00349 (40596) covalent geometry : angle 0.61303 (54938) SS BOND : bond 0.00753 ( 1) SS BOND : angle 1.75177 ( 2) hydrogen bonds : bond 0.05572 ( 1973) hydrogen bonds : angle 4.39564 ( 5640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21361.11 seconds wall clock time: 362 minutes 17.36 seconds (21737.36 seconds total)