Starting phenix.real_space_refine on Sun Feb 8 03:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnf_44726/02_2026/9bnf_44726.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 24837 2.51 5 N 6381 2.21 5 O 7521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38931 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7840 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4864 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 569} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 7851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7851 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 952} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "F" Number of atoms: 7838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7838 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 9.02, per 1000 atoms: 0.23 Number of scatterers: 38931 At special positions: 0 Unit cell: (178.048, 152.256, 234.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 7521 8.00 N 6381 7.00 C 24837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 234 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 234 " " NAG D1304 " - " ASN D 282 " " NAG D1305 " - " ASN D 343 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D1074 " " NAG D1310 " - " ASN D1134 " " NAG D1311 " - " ASN D 165 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 234 " " NAG F1304 " - " ASN F 282 " " NAG F1305 " - " ASN F 343 " " NAG F1306 " - " ASN F 616 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F 709 " " NAG F1309 " - " ASN F1074 " " NAG F1310 " - " ASN F1134 " " NAG F1311 " - " ASN F 165 " " NAG G 1 " - " ASN D1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN D 331 " " NAG L 1 " - " ASN D 717 " " NAG M 1 " - " ASN D 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN F 331 " " NAG P 1 " - " ASN F 717 " " NAG Q 1 " - " ASN F 801 " " NAG R 1 " - " ASN F1098 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9044 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 59 sheets defined 41.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 82 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.900A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.510A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.910A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.997A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.580A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.673A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.182A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.593A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.271A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.789A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.936A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.502A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.988A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.598A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.597A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.185A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.052A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.629A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.550A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 20 through 53 Processing helix chain 'C' and resid 55 through 82 removed outlier: 4.274A pdb=" N MET C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.842A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.643A pdb=" N SER C 106 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 129 Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 172 through 194 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 218 through 252 removed outlier: 3.584A pdb=" N ILE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.049A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 400 through 413 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.412A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 removed outlier: 4.339A pdb=" N MET C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 removed outlier: 3.539A pdb=" N SER C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 534 removed outlier: 4.115A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 561 removed outlier: 3.737A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 561 " --> pdb=" O MET C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.614A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 383 through 388 removed outlier: 4.259A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.685A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.550A pdb=" N GLU D 619 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 756 removed outlier: 3.713A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.148A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 912 through 918 removed outlier: 4.036A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.568A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1145 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.730A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.603A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.829A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.577A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.527A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.726A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.840A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.525A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 414 removed outlier: 3.967A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 482 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.373A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.790A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 560 " --> pdb=" O ASN E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 Processing helix chain 'E' and resid 581 through 599 Proline residue: E 590 - end of helix Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 337 through 342 removed outlier: 4.181A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 370 removed outlier: 3.775A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.983A pdb=" N ASP F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.562A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 755 removed outlier: 3.725A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 758 through 783 Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.505A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 912 through 918 removed outlier: 4.138A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1032 removed outlier: 4.451A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.381A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.635A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.856A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.748A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.982A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.852A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AB4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AB5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.672A pdb=" N PHE B 565 " --> pdb=" O PHE F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.612A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.789A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.876A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AC3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.383A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AC8, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.923A pdb=" N ASN D 188 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AD1, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.956A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU D 244 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 84 through 85 removed outlier: 7.074A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL D 126 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.781A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AD6, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AE1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 711 through 715 removed outlier: 4.174A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.823A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 718 through 728 Processing sheet with id=AE5, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.496A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AE8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.445A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.123A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA F 264 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N HIS F 207 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N LEU F 223 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 48 through 55 removed outlier: 3.798A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AF4, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.594A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 311 through 319 removed outlier: 6.756A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AF7, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AF8, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.909A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'F' and resid 653 through 655 removed outlier: 6.659A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.795A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN F 717 " --> pdb=" O ALA F1070 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 1047 through 1050 removed outlier: 7.007A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.367A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 1081 through 1082 1869 hydrogen bonds defined for protein. 5253 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: 10.21 Time building geometry restraints manager: 4.63 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: 10505 1.33 - 1.46: 10732 1.46 - 1.58: 18369 1.58 - 1.71: 0 1.71 - 1.84: 279 Bond restraints: 39885 Sorted by residual: bond pdb=" C1 NAG F1309 " pdb=" O5 NAG F1309 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.18e-02 7.18e+03 8.22e+00 ... (remaining 39880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 53647 2.51 - 5.02: 555 5.02 - 7.54: 49 7.54 - 10.05: 10 10.05 - 12.56: 4 Bond angle restraints: 54265 Sorted by residual: angle pdb=" C ASN B 87 " pdb=" CA ASN B 87 " pdb=" CB ASN B 87 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C PHE F 32 " pdb=" CA PHE F 32 " pdb=" CB PHE F 32 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 angle pdb=" CB MET A 376 " pdb=" CG MET A 376 " pdb=" SD MET A 376 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N LYS E 465 " pdb=" CA LYS E 465 " pdb=" C LYS E 465 " ideal model delta sigma weight residual 113.19 108.74 4.45 1.19e+00 7.06e-01 1.40e+01 angle pdb=" CA ASN B 87 " pdb=" C ASN B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 119.98 116.81 3.17 8.50e-01 1.38e+00 1.39e+01 ... (remaining 54260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 22948 24.82 - 49.63: 1246 49.63 - 74.45: 153 74.45 - 99.26: 45 99.26 - 124.08: 33 Dihedral angle restraints: 24425 sinusoidal: 10382 harmonic: 14043 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 30.34 62.66 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual -86.00 -134.33 48.33 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CA SER D1097 " pdb=" C SER D1097 " pdb=" N ASN D1098 " pdb=" CA ASN D1098 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 24422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 5934 0.102 - 0.204: 213 0.204 - 0.306: 7 0.306 - 0.407: 1 0.407 - 0.509: 2 Chirality restraints: 6157 Sorted by residual: chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG F1303 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG F1303 " pdb=" O5 NAG F1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN F 331 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 6154 not shown) Planarity restraints: 6999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 458 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LYS C 458 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS C 458 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP C 459 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 951 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C VAL B 951 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 951 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 952 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO B 987 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.023 5.00e-02 4.00e+02 ... (remaining 6996 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1160 2.69 - 3.24: 40383 3.24 - 3.80: 68258 3.80 - 4.35: 85621 4.35 - 4.90: 139221 Nonbonded interactions: 334643 Sorted by model distance: nonbonded pdb=" NH2 ARG D 34 " pdb=" O PRO D 217 " model vdw 2.141 3.120 nonbonded pdb=" OH TYR D 37 " pdb=" O LEU D 54 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" OG1 THR D 500 " model vdw 2.175 3.040 nonbonded pdb=" O GLY F 880 " pdb=" OG SER F 884 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR D 91 " pdb=" OE2 GLU D 191 " model vdw 2.183 3.040 ... (remaining 334638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 508 or (resid 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 641)) selection = chain 'C' selection = (chain 'E' and (resid 19 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 508 or (resid 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 615)) } ncs_group { reference = (chain 'B' and (resid 27 through 579 or (resid 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 883 or (resid 884 and (name N o \ r name CA or name C or name O or name CB )) or resid 885 through 911 or (resid 9 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 913 through \ 1311)) selection = (chain 'D' and (resid 27 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 579 or (resid 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 through 710 or (resid 7 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 712 through \ 911 or (resid 912 and (name N or name CA or name C or name O or name CB )) or r \ esid 913 through 1144 or resid 1301 through 1311)) selection = (chain 'F' and (resid 27 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 710 or (resid 711 and (name N o \ r name CA or name C or name O or name CB )) or resid 712 through 883 or (resid 8 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 885 through \ 1311)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=1.00 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: 3.660 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.460 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.004 0.075 39987 Z= 0.206 Angle : 0.638 16.077 54526 Z= 0.317 Chirality : 0.045 0.509 6157 Planarity : 0.003 0.041 6954 Dihedral : 15.499 124.077 15246 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 0.40 % Allowed : 9.14 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.60 (0.13), residues: 4756 helix: 2.06 (0.13), residues: 1763 sheet: -0.81 (0.18), residues: 789 loop : -0.47 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 466 TYR 0.018 0.001 TYR C 385 PHE 0.016 0.001 PHE F 342 TRP 0.016 0.001 TRP D 64 HIS 0.007 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00420 (39885) covalent geometry : angle 0.60246 (54265) SS BOND : bond 0.00237 ( 45) SS BOND : angle 0.70255 ( 90) hydrogen bonds : bond 0.12047 ( 1843) hydrogen bonds : angle 6.12264 ( 5253) link_BETA1-4 : bond 0.00646 ( 12) link_BETA1-4 : angle 3.28291 ( 36) link_NAG-ASN : bond 0.00707 ( 45) link_NAG-ASN : angle 3.88260 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.4617 (mtp) cc_final: -0.4975 (tpt) REVERT: E 123 MET cc_start: -0.3023 (ttt) cc_final: -0.4247 (ptp) REVERT: E 183 TYR cc_start: 0.4047 (OUTLIER) cc_final: 0.2805 (t80) REVERT: E 474 MET cc_start: -0.1709 (tpp) cc_final: -0.3005 (tpp) REVERT: F 338 PHE cc_start: 0.8263 (m-10) cc_final: 0.8038 (m-10) REVERT: F 614 ASP cc_start: 0.8499 (t0) cc_final: 0.8070 (t0) REVERT: F 699 LEU cc_start: 0.9317 (mt) cc_final: 0.8873 (mt) outliers start: 17 outliers final: 7 residues processed: 138 average time/residue: 0.2436 time to fit residues: 57.7396 Evaluate side-chains 132 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain F residue 343 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN D 239 GLN E 53 ASN E 58 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.113061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068959 restraints weight = 179042.936| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.43 r_work: 0.2812 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39987 Z= 0.199 Angle : 0.608 13.208 54526 Z= 0.293 Chirality : 0.044 0.460 6157 Planarity : 0.004 0.048 6954 Dihedral : 10.366 111.840 6370 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.93 % Allowed : 9.90 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.67 (0.12), residues: 4756 helix: 2.09 (0.12), residues: 1772 sheet: -0.77 (0.18), residues: 787 loop : -0.42 (0.14), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 328 TYR 0.018 0.001 TYR C 385 PHE 0.020 0.001 PHE B 342 TRP 0.017 0.001 TRP D 64 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00441 (39885) covalent geometry : angle 0.57735 (54265) SS BOND : bond 0.00245 ( 45) SS BOND : angle 0.74281 ( 90) hydrogen bonds : bond 0.03953 ( 1843) hydrogen bonds : angle 5.14573 ( 5253) link_BETA1-4 : bond 0.00563 ( 12) link_BETA1-4 : angle 2.72139 ( 36) link_NAG-ASN : bond 0.00671 ( 45) link_NAG-ASN : angle 3.63331 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.0945 (mtp) cc_final: -0.2599 (mmm) REVERT: A 480 MET cc_start: 0.3001 (ptt) cc_final: 0.2082 (mtm) REVERT: C 152 MET cc_start: -0.0097 (mpp) cc_final: -0.0888 (mpp) REVERT: E 62 MET cc_start: 0.7762 (mmm) cc_final: 0.7524 (mmm) REVERT: E 123 MET cc_start: -0.1202 (OUTLIER) cc_final: -0.3368 (ptp) REVERT: E 183 TYR cc_start: 0.4657 (OUTLIER) cc_final: 0.3427 (t80) REVERT: E 480 MET cc_start: 0.6396 (ppp) cc_final: 0.5721 (ppp) REVERT: F 341 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8737 (m) REVERT: F 342 PHE cc_start: 0.9447 (m-80) cc_final: 0.8985 (m-80) REVERT: F 345 THR cc_start: 0.5549 (OUTLIER) cc_final: 0.5080 (p) REVERT: F 614 ASP cc_start: 0.8983 (t0) cc_final: 0.8579 (t0) outliers start: 39 outliers final: 15 residues processed: 163 average time/residue: 0.2080 time to fit residues: 59.9766 Evaluate side-chains 144 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 315 optimal weight: 6.9990 chunk 18 optimal weight: 50.0000 chunk 292 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 452 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 333 optimal weight: 50.0000 chunk 80 optimal weight: 1.9990 chunk 406 optimal weight: 6.9990 chunk 471 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.113190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.071876 restraints weight = 178338.256| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.87 r_work: 0.2830 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39987 Z= 0.165 Angle : 0.583 13.158 54526 Z= 0.278 Chirality : 0.043 0.456 6157 Planarity : 0.003 0.040 6954 Dihedral : 8.495 110.262 6359 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 10.78 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.74 (0.12), residues: 4756 helix: 2.16 (0.12), residues: 1772 sheet: -0.67 (0.18), residues: 773 loop : -0.42 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 328 TYR 0.024 0.001 TYR D 636 PHE 0.017 0.001 PHE B 342 TRP 0.016 0.001 TRP D 64 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00364 (39885) covalent geometry : angle 0.55349 (54265) SS BOND : bond 0.00192 ( 45) SS BOND : angle 0.69070 ( 90) hydrogen bonds : bond 0.03651 ( 1843) hydrogen bonds : angle 4.93485 ( 5253) link_BETA1-4 : bond 0.00608 ( 12) link_BETA1-4 : angle 2.75041 ( 36) link_NAG-ASN : bond 0.00604 ( 45) link_NAG-ASN : angle 3.43454 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.0188 (mtp) cc_final: -0.1658 (mmm) REVERT: A 332 MET cc_start: 0.5837 (ppp) cc_final: 0.5634 (ppp) REVERT: A 480 MET cc_start: 0.3005 (ptt) cc_final: 0.2018 (mtm) REVERT: C 383 MET cc_start: 0.8068 (ptm) cc_final: 0.7740 (mtt) REVERT: D 64 TRP cc_start: 0.9137 (OUTLIER) cc_final: 0.8903 (t-100) REVERT: D 900 MET cc_start: 0.9404 (mtt) cc_final: 0.9199 (mtt) REVERT: D 1019 ARG cc_start: 0.9274 (tpt170) cc_final: 0.8951 (tpt90) REVERT: E 62 MET cc_start: 0.8290 (mmm) cc_final: 0.8047 (mmm) REVERT: E 123 MET cc_start: -0.0358 (OUTLIER) cc_final: -0.2532 (ptp) REVERT: E 383 MET cc_start: 0.8677 (ppp) cc_final: 0.8161 (ptm) REVERT: E 480 MET cc_start: 0.6493 (ppp) cc_final: 0.5903 (ppp) REVERT: F 341 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8657 (m) REVERT: F 342 PHE cc_start: 0.9345 (m-80) cc_final: 0.8925 (m-80) REVERT: F 345 THR cc_start: 0.5709 (OUTLIER) cc_final: 0.5177 (p) REVERT: F 614 ASP cc_start: 0.8974 (t0) cc_final: 0.8543 (t0) REVERT: F 864 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9201 (tp) outliers start: 59 outliers final: 26 residues processed: 185 average time/residue: 0.2160 time to fit residues: 71.2002 Evaluate side-chains 157 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 864 LEU Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 202 optimal weight: 10.0000 chunk 378 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 0.0270 chunk 350 optimal weight: 40.0000 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 177 optimal weight: 50.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1083 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4302 r_free = 0.4302 target = 0.112995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070395 restraints weight = 177989.727| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 5.25 r_work: 0.2804 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 39987 Z= 0.204 Angle : 0.591 12.920 54526 Z= 0.284 Chirality : 0.043 0.453 6157 Planarity : 0.003 0.041 6954 Dihedral : 7.777 110.602 6351 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.69 % Allowed : 11.54 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.74 (0.12), residues: 4756 helix: 2.17 (0.12), residues: 1772 sheet: -0.67 (0.18), residues: 775 loop : -0.42 (0.14), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 169 TYR 0.018 0.001 TYR F1067 PHE 0.016 0.001 PHE A 32 TRP 0.016 0.001 TRP D 64 HIS 0.008 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00454 (39885) covalent geometry : angle 0.56308 (54265) SS BOND : bond 0.00224 ( 45) SS BOND : angle 0.68083 ( 90) hydrogen bonds : bond 0.03605 ( 1843) hydrogen bonds : angle 4.91151 ( 5253) link_BETA1-4 : bond 0.00546 ( 12) link_BETA1-4 : angle 2.75040 ( 36) link_NAG-ASN : bond 0.00606 ( 45) link_NAG-ASN : angle 3.36300 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 127 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.1778 (mtp) cc_final: -0.0411 (mmt) REVERT: A 332 MET cc_start: 0.5935 (ppp) cc_final: 0.5674 (ppp) REVERT: A 480 MET cc_start: 0.3155 (ptt) cc_final: 0.2252 (mtm) REVERT: B 239 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7452 (tp40) REVERT: C 366 MET cc_start: 0.5179 (tpt) cc_final: 0.3560 (mtp) REVERT: D 64 TRP cc_start: 0.9151 (OUTLIER) cc_final: 0.8870 (t-100) REVERT: D 101 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9200 (tt) REVERT: D 900 MET cc_start: 0.9414 (mtt) cc_final: 0.9200 (mtt) REVERT: D 1019 ARG cc_start: 0.9268 (tpt170) cc_final: 0.8906 (tpt90) REVERT: E 62 MET cc_start: 0.8328 (mmm) cc_final: 0.8126 (mmm) REVERT: E 123 MET cc_start: 0.0290 (OUTLIER) cc_final: -0.2235 (ptp) REVERT: E 383 MET cc_start: 0.8701 (ppp) cc_final: 0.8281 (ptm) REVERT: E 480 MET cc_start: 0.6601 (ppp) cc_final: 0.6057 (ppp) REVERT: F 341 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8696 (m) REVERT: F 342 PHE cc_start: 0.9379 (m-80) cc_final: 0.8983 (m-80) REVERT: F 345 THR cc_start: 0.5845 (OUTLIER) cc_final: 0.5276 (p) REVERT: F 614 ASP cc_start: 0.9009 (t0) cc_final: 0.8575 (t0) outliers start: 71 outliers final: 35 residues processed: 194 average time/residue: 0.2076 time to fit residues: 71.7922 Evaluate side-chains 167 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 98 optimal weight: 50.0000 chunk 237 optimal weight: 2.9990 chunk 331 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 chunk 452 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.113055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071159 restraints weight = 177867.528| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.85 r_work: 0.2779 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39987 Z= 0.192 Angle : 0.588 12.836 54526 Z= 0.282 Chirality : 0.043 0.451 6157 Planarity : 0.003 0.041 6954 Dihedral : 7.374 109.581 6351 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 12.16 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.74 (0.12), residues: 4756 helix: 2.18 (0.12), residues: 1769 sheet: -0.66 (0.18), residues: 777 loop : -0.43 (0.14), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 169 TYR 0.018 0.001 TYR F1067 PHE 0.018 0.001 PHE B 342 TRP 0.015 0.001 TRP D 64 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00428 (39885) covalent geometry : angle 0.56168 (54265) SS BOND : bond 0.00211 ( 45) SS BOND : angle 0.65891 ( 90) hydrogen bonds : bond 0.03553 ( 1843) hydrogen bonds : angle 4.86713 ( 5253) link_BETA1-4 : bond 0.00586 ( 12) link_BETA1-4 : angle 2.75465 ( 36) link_NAG-ASN : bond 0.00582 ( 45) link_NAG-ASN : angle 3.27504 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.0012 (mtp) cc_final: -0.1950 (mmt) REVERT: A 249 MET cc_start: 0.5964 (ptp) cc_final: 0.5705 (mpp) REVERT: A 332 MET cc_start: 0.5773 (ppp) cc_final: 0.5497 (ppp) REVERT: A 480 MET cc_start: 0.3141 (ptt) cc_final: 0.2116 (mtm) REVERT: B 239 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7484 (tp40) REVERT: C 323 MET cc_start: 0.7335 (ppp) cc_final: 0.7013 (ppp) REVERT: C 366 MET cc_start: 0.5190 (tpt) cc_final: 0.3573 (mtp) REVERT: C 383 MET cc_start: 0.7960 (ptm) cc_final: 0.7595 (mtt) REVERT: D 64 TRP cc_start: 0.9164 (OUTLIER) cc_final: 0.8855 (t-100) REVERT: D 101 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9201 (tt) REVERT: D 1019 ARG cc_start: 0.9326 (tpt170) cc_final: 0.8974 (tpt90) REVERT: E 123 MET cc_start: -0.0051 (OUTLIER) cc_final: -0.2304 (ptp) REVERT: E 249 MET cc_start: 0.5620 (mmp) cc_final: 0.5409 (mmt) REVERT: E 480 MET cc_start: 0.6464 (ppp) cc_final: 0.5906 (ppp) REVERT: F 341 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8741 (m) REVERT: F 342 PHE cc_start: 0.9391 (m-80) cc_final: 0.8995 (m-80) REVERT: F 345 THR cc_start: 0.6036 (OUTLIER) cc_final: 0.5465 (p) REVERT: F 614 ASP cc_start: 0.9052 (t0) cc_final: 0.8650 (t0) outliers start: 64 outliers final: 39 residues processed: 186 average time/residue: 0.2096 time to fit residues: 70.2566 Evaluate side-chains 172 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 469 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 380 optimal weight: 0.0770 chunk 376 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 215 optimal weight: 50.0000 chunk 454 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 overall best weight: 2.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** 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 = 0.4308 r_free = 0.4308 target = 0.113250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071506 restraints weight = 178946.141| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 6.07 r_work: 0.2782 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39987 Z= 0.158 Angle : 0.570 12.794 54526 Z= 0.273 Chirality : 0.043 0.453 6157 Planarity : 0.003 0.040 6954 Dihedral : 7.081 108.828 6351 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.54 % Allowed : 12.75 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.79 (0.12), residues: 4756 helix: 2.21 (0.12), residues: 1767 sheet: -0.60 (0.18), residues: 773 loop : -0.41 (0.14), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.023 0.001 TYR D 636 PHE 0.016 0.001 PHE B 342 TRP 0.015 0.001 TRP D 64 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00351 (39885) covalent geometry : angle 0.54380 (54265) SS BOND : bond 0.00181 ( 45) SS BOND : angle 0.61380 ( 90) hydrogen bonds : bond 0.03484 ( 1843) hydrogen bonds : angle 4.79703 ( 5253) link_BETA1-4 : bond 0.00600 ( 12) link_BETA1-4 : angle 2.73674 ( 36) link_NAG-ASN : bond 0.00543 ( 45) link_NAG-ASN : angle 3.19534 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 129 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.1155 (mtp) cc_final: -0.1013 (mmt) REVERT: A 249 MET cc_start: 0.6052 (ptp) cc_final: 0.5831 (mpp) REVERT: A 332 MET cc_start: 0.5895 (ppp) cc_final: 0.5588 (ppp) REVERT: A 480 MET cc_start: 0.3379 (ptt) cc_final: 0.2455 (mtm) REVERT: B 201 PHE cc_start: 0.9165 (t80) cc_final: 0.8908 (t80) REVERT: B 239 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: C 366 MET cc_start: 0.5242 (tpt) cc_final: 0.3755 (mtp) REVERT: D 64 TRP cc_start: 0.9167 (OUTLIER) cc_final: 0.8934 (t-100) REVERT: D 1019 ARG cc_start: 0.9319 (tpt170) cc_final: 0.8934 (tpt90) REVERT: E 123 MET cc_start: 0.0193 (OUTLIER) cc_final: -0.2072 (ptp) REVERT: E 249 MET cc_start: 0.5719 (mmp) cc_final: 0.5486 (mmt) REVERT: E 480 MET cc_start: 0.6627 (ppp) cc_final: 0.6122 (ppp) REVERT: F 342 PHE cc_start: 0.9454 (m-80) cc_final: 0.9121 (m-80) REVERT: F 345 THR cc_start: 0.6057 (OUTLIER) cc_final: 0.5524 (p) REVERT: F 614 ASP cc_start: 0.9026 (t0) cc_final: 0.8632 (t0) outliers start: 65 outliers final: 43 residues processed: 190 average time/residue: 0.2181 time to fit residues: 73.8436 Evaluate side-chains 173 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 475 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 462 optimal weight: 0.9990 chunk 422 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 318 optimal weight: 70.0000 chunk 167 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.113020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071053 restraints weight = 178554.559| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.81 r_work: 0.2774 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39987 Z= 0.185 Angle : 0.585 12.605 54526 Z= 0.281 Chirality : 0.043 0.447 6157 Planarity : 0.003 0.041 6954 Dihedral : 6.922 108.614 6349 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 13.22 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.80 (0.12), residues: 4756 helix: 2.24 (0.12), residues: 1761 sheet: -0.63 (0.18), residues: 773 loop : -0.40 (0.14), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.018 0.001 TYR F1067 PHE 0.016 0.001 PHE B 342 TRP 0.015 0.001 TRP D 64 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00412 (39885) covalent geometry : angle 0.56003 (54265) SS BOND : bond 0.00198 ( 45) SS BOND : angle 0.61253 ( 90) hydrogen bonds : bond 0.03493 ( 1843) hydrogen bonds : angle 4.80651 ( 5253) link_BETA1-4 : bond 0.00578 ( 12) link_BETA1-4 : angle 2.72621 ( 36) link_NAG-ASN : bond 0.00544 ( 45) link_NAG-ASN : angle 3.11908 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.1471 (mtp) cc_final: -0.2986 (mmt) REVERT: A 332 MET cc_start: 0.5598 (ppp) cc_final: 0.5219 (ppp) REVERT: A 480 MET cc_start: 0.3169 (ptt) cc_final: 0.2070 (mtm) REVERT: B 239 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7309 (tp40) REVERT: B 957 GLN cc_start: 0.9476 (mm-40) cc_final: 0.9166 (tt0) REVERT: C 323 MET cc_start: 0.7185 (ppp) cc_final: 0.6560 (ppp) REVERT: C 366 MET cc_start: 0.5033 (tpt) cc_final: 0.3438 (mtp) REVERT: D 64 TRP cc_start: 0.9171 (OUTLIER) cc_final: 0.8812 (t-100) REVERT: D 101 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9203 (tt) REVERT: E 123 MET cc_start: -0.0524 (OUTLIER) cc_final: -0.2365 (ptp) REVERT: E 249 MET cc_start: 0.5410 (mmp) cc_final: 0.5139 (mmt) REVERT: E 480 MET cc_start: 0.6567 (ppp) cc_final: 0.5973 (ppp) REVERT: F 345 THR cc_start: 0.6000 (OUTLIER) cc_final: 0.5436 (p) REVERT: F 614 ASP cc_start: 0.9036 (t0) cc_final: 0.8643 (t0) outliers start: 64 outliers final: 50 residues processed: 188 average time/residue: 0.1972 time to fit residues: 66.4123 Evaluate side-chains 181 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 363 optimal weight: 0.2980 chunk 232 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 182 optimal weight: 7.9990 chunk 458 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 50.0000 chunk 235 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.112927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070446 restraints weight = 178893.814| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.27 r_work: 0.2817 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39987 Z= 0.188 Angle : 0.587 12.495 54526 Z= 0.282 Chirality : 0.043 0.444 6157 Planarity : 0.003 0.042 6954 Dihedral : 6.780 108.345 6349 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.66 % Allowed : 13.37 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.80 (0.12), residues: 4756 helix: 2.25 (0.12), residues: 1756 sheet: -0.65 (0.18), residues: 775 loop : -0.39 (0.14), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 245 TYR 0.018 0.001 TYR F1067 PHE 0.016 0.001 PHE B 342 TRP 0.016 0.001 TRP D 64 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00417 (39885) covalent geometry : angle 0.56268 (54265) SS BOND : bond 0.00198 ( 45) SS BOND : angle 0.60728 ( 90) hydrogen bonds : bond 0.03501 ( 1843) hydrogen bonds : angle 4.81804 ( 5253) link_BETA1-4 : bond 0.00545 ( 12) link_BETA1-4 : angle 2.72508 ( 36) link_NAG-ASN : bond 0.00538 ( 45) link_NAG-ASN : angle 3.09559 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.0686 (mtp) cc_final: -0.2408 (mmt) REVERT: A 332 MET cc_start: 0.5762 (ppp) cc_final: 0.5397 (ppp) REVERT: A 480 MET cc_start: 0.3337 (ptt) cc_final: 0.2252 (mtm) REVERT: B 239 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7357 (tp40) REVERT: B 957 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9177 (tt0) REVERT: C 323 MET cc_start: 0.7465 (ppp) cc_final: 0.6899 (ppp) REVERT: C 366 MET cc_start: 0.5239 (tpt) cc_final: 0.3749 (mtp) REVERT: D 64 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.8793 (t-100) REVERT: D 101 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9219 (tt) REVERT: D 1019 ARG cc_start: 0.9300 (tpt170) cc_final: 0.9017 (tpt90) REVERT: E 123 MET cc_start: -0.0098 (OUTLIER) cc_final: -0.2184 (ptp) REVERT: E 249 MET cc_start: 0.5503 (mmp) cc_final: 0.5097 (mmt) REVERT: E 480 MET cc_start: 0.6522 (ppp) cc_final: 0.5961 (ppp) REVERT: F 474 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: F 614 ASP cc_start: 0.9030 (t0) cc_final: 0.8646 (t0) outliers start: 70 outliers final: 52 residues processed: 193 average time/residue: 0.2108 time to fit residues: 72.6207 Evaluate side-chains 182 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 53 optimal weight: 50.0000 chunk 79 optimal weight: 0.0670 chunk 326 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 55 optimal weight: 50.0000 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 40.0000 chunk 328 optimal weight: 30.0000 chunk 376 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 overall best weight: 3.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.112796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070378 restraints weight = 179327.114| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.57 r_work: 0.2783 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39987 Z= 0.197 Angle : 0.595 12.358 54526 Z= 0.287 Chirality : 0.043 0.439 6157 Planarity : 0.003 0.042 6954 Dihedral : 6.650 108.234 6349 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.61 % Allowed : 13.44 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.79 (0.12), residues: 4756 helix: 2.24 (0.12), residues: 1761 sheet: -0.68 (0.18), residues: 775 loop : -0.39 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1091 TYR 0.024 0.001 TYR D 636 PHE 0.015 0.001 PHE B 342 TRP 0.016 0.001 TRP D 64 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00438 (39885) covalent geometry : angle 0.57137 (54265) SS BOND : bond 0.00206 ( 45) SS BOND : angle 0.61444 ( 90) hydrogen bonds : bond 0.03517 ( 1843) hydrogen bonds : angle 4.82433 ( 5253) link_BETA1-4 : bond 0.00549 ( 12) link_BETA1-4 : angle 2.72373 ( 36) link_NAG-ASN : bond 0.00545 ( 45) link_NAG-ASN : angle 3.08515 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.1607 (mtp) cc_final: -0.3365 (mmm) REVERT: A 332 MET cc_start: 0.5694 (ppp) cc_final: 0.5296 (ppp) REVERT: A 480 MET cc_start: 0.3229 (ptt) cc_final: 0.2051 (mtm) REVERT: B 239 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7289 (tp40) REVERT: B 957 GLN cc_start: 0.9484 (mm-40) cc_final: 0.9177 (tt0) REVERT: C 323 MET cc_start: 0.7413 (ppp) cc_final: 0.6805 (ppp) REVERT: C 332 MET cc_start: 0.6625 (ptt) cc_final: 0.5832 (ptt) REVERT: C 366 MET cc_start: 0.5236 (tpt) cc_final: 0.3661 (mtp) REVERT: D 64 TRP cc_start: 0.9129 (OUTLIER) cc_final: 0.8731 (t-100) REVERT: D 101 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9225 (mp) REVERT: D 1019 ARG cc_start: 0.9279 (tpt170) cc_final: 0.8935 (tpt90) REVERT: E 123 MET cc_start: -0.0543 (OUTLIER) cc_final: -0.2371 (ptp) REVERT: E 249 MET cc_start: 0.5402 (mmp) cc_final: 0.4960 (mmt) REVERT: E 474 MET cc_start: 0.1552 (tpp) cc_final: 0.0703 (tpp) REVERT: E 480 MET cc_start: 0.6445 (ppp) cc_final: 0.5825 (ppp) REVERT: F 345 THR cc_start: 0.6193 (OUTLIER) cc_final: 0.5665 (p) REVERT: F 474 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: F 614 ASP cc_start: 0.9079 (t0) cc_final: 0.8708 (t0) outliers start: 68 outliers final: 55 residues processed: 186 average time/residue: 0.2053 time to fit residues: 68.5093 Evaluate side-chains 183 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 501 ASN Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 413 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 134 optimal weight: 0.0170 chunk 209 optimal weight: 10.0000 chunk 372 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 377 optimal weight: 0.1980 chunk 75 optimal weight: 5.9990 overall best weight: 2.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.113009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070897 restraints weight = 177924.989| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 5.88 r_work: 0.2778 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.004 0.057 39987 Z= 0.163 Angle : 0.587 12.382 54526 Z= 0.283 Chirality : 0.043 0.440 6157 Planarity : 0.003 0.041 6954 Dihedral : 6.566 107.975 6349 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.40 % Allowed : 13.79 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.81 (0.12), residues: 4756 helix: 2.25 (0.12), residues: 1761 sheet: -0.64 (0.18), residues: 772 loop : -0.38 (0.14), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.018 0.001 TYR F1067 PHE 0.027 0.001 PHE F 338 TRP 0.015 0.001 TRP D 64 HIS 0.014 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00364 (39885) covalent geometry : angle 0.56401 (54265) SS BOND : bond 0.00179 ( 45) SS BOND : angle 0.59370 ( 90) hydrogen bonds : bond 0.03467 ( 1843) hydrogen bonds : angle 4.80767 ( 5253) link_BETA1-4 : bond 0.00591 ( 12) link_BETA1-4 : angle 2.71553 ( 36) link_NAG-ASN : bond 0.00513 ( 45) link_NAG-ASN : angle 3.05496 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: -0.0091 (mtp) cc_final: -0.1464 (mmt) REVERT: A 332 MET cc_start: 0.5978 (ppp) cc_final: 0.5637 (ppp) REVERT: A 480 MET cc_start: 0.3471 (ptt) cc_final: 0.2454 (mtm) REVERT: B 239 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7410 (tp40) REVERT: B 957 GLN cc_start: 0.9498 (mm-40) cc_final: 0.9203 (tt0) REVERT: C 123 MET cc_start: 0.3029 (mmt) cc_final: 0.0627 (mtp) REVERT: C 323 MET cc_start: 0.7668 (ppp) cc_final: 0.7187 (ppp) REVERT: C 366 MET cc_start: 0.5525 (tpt) cc_final: 0.4078 (mtp) REVERT: D 64 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.8780 (t-100) REVERT: D 101 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9227 (mp) REVERT: D 1019 ARG cc_start: 0.9285 (tpt170) cc_final: 0.9041 (tpt90) REVERT: E 123 MET cc_start: 0.0390 (OUTLIER) cc_final: -0.1936 (ptp) REVERT: E 249 MET cc_start: 0.5617 (mmp) cc_final: 0.5243 (mmt) REVERT: E 480 MET cc_start: 0.6524 (ppp) cc_final: 0.5960 (ppp) REVERT: F 345 THR cc_start: 0.5953 (OUTLIER) cc_final: 0.5430 (p) REVERT: F 474 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.5924 (tm-30) REVERT: F 614 ASP cc_start: 0.9067 (t0) cc_final: 0.8691 (t0) REVERT: F 869 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.9122 (mtm) outliers start: 59 outliers final: 49 residues processed: 178 average time/residue: 0.2130 time to fit residues: 67.3685 Evaluate side-chains 178 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 501 ASN Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 460 ARG Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 247 optimal weight: 6.9990 chunk 228 optimal weight: 40.0000 chunk 316 optimal weight: 0.7980 chunk 107 optimal weight: 0.0370 chunk 321 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.112915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070776 restraints weight = 178278.137| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 5.89 r_work: 0.2784 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 39987 Z= 0.166 Angle : 0.668 59.192 54526 Z= 0.344 Chirality : 0.043 0.440 6157 Planarity : 0.003 0.042 6954 Dihedral : 6.572 107.989 6349 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 1.50 % Allowed : 13.70 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: 0.81 (0.12), residues: 4756 helix: 2.25 (0.12), residues: 1761 sheet: -0.64 (0.18), residues: 772 loop : -0.39 (0.14), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.018 0.001 TYR F1067 PHE 0.017 0.001 PHE F 338 TRP 0.015 0.001 TRP D 64 HIS 0.013 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00367 (39885) covalent geometry : angle 0.64798 (54265) SS BOND : bond 0.00178 ( 45) SS BOND : angle 0.60464 ( 90) hydrogen bonds : bond 0.03466 ( 1843) hydrogen bonds : angle 4.81143 ( 5253) link_BETA1-4 : bond 0.00628 ( 12) link_BETA1-4 : angle 2.74921 ( 36) link_NAG-ASN : bond 0.00514 ( 45) link_NAG-ASN : angle 3.05283 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17876.85 seconds wall clock time: 304 minutes 38.15 seconds (18278.15 seconds total)