Starting phenix.real_space_refine on Sun Feb 8 03:40:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bng_44727/02_2026/9bng_44727.map" } resolution = 3.73 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= 0.011 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 186 5.16 5 C 24736 2.51 5 N 6368 2.21 5 O 7489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s 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: 38779 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: 7839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7839 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 7829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7829 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 952} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 4838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4838 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7815 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 30 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: "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: "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: "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: "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: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.68, per 1000 atoms: 0.22 Number of scatterers: 38779 At special positions: 0 Unit cell: (158.158, 179.014, 232.892, 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 186 16.00 O 7489 8.00 N 6368 7.00 C 24736 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=2.02 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=2.02 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=2.03 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 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 343 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 125 " " NAG D1303 " - " ASN D 234 " " NAG D1304 " - " ASN D 343 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG D1309 " - " ASN D1134 " " NAG F1301 " - " ASN F 122 " " NAG F1302 " - " ASN F 234 " " NAG F1303 " - " ASN F 282 " " NAG F1304 " - " ASN F 616 " " NAG F1305 " - " ASN F 657 " " NAG F1306 " - " ASN F 709 " " NAG F1307 " - " ASN F1074 " " NAG F1308 " - " ASN F1098 " " NAG G 1 " - " ASN B 331 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN D 282 " " NAG L 1 " - " ASN D 717 " " NAG M 1 " - " ASN D 801 " " NAG N 1 " - " ASN F 165 " " NAG O 1 " - " ASN F 331 " " NAG P 1 " - " ASN F 343 " " NAG Q 1 " - " ASN F 717 " " NAG R 1 " - " ASN F 801 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9040 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 55 sheets defined 42.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.924A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.968A pdb=" N MET A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.594A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.518A 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 154 Processing helix chain 'A' and resid 157 through 172 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 removed outlier: 3.758A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 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: 4.184A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.623A 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 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.283A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 484 removed outlier: 4.579A pdb=" N MET A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.370A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.813A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.590A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.296A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.637A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.946A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 529 through 533 removed outlier: 4.126A pdb=" N ASN B 532 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 533 " --> pdb=" O SER B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 529 through 533' Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.610A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.671A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (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: 3.658A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.954A 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 966 removed outlier: 3.632A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.293A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.827A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 82 removed outlier: 3.891A pdb=" N MET C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.561A pdb=" N SER C 106 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 146 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: 3.779A 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 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' 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: 4.061A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 Processing helix chain 'C' and resid 389 through 393 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 447 Processing helix chain 'C' and resid 449 through 465 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.890A pdb=" N GLU C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 509 Processing helix chain 'C' and resid 512 through 534 removed outlier: 4.366A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.972A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 581 through 599 Proline residue: C 590 - end of helix Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.894A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 4.120A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.913A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP D 389 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 removed outlier: 3.511A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.721A pdb=" N GLU D 619 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 747 through 756 removed outlier: 3.692A 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: 3.846A 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 919 removed outlier: 3.963A 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 966 removed outlier: 3.761A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.508A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.837A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 4.089A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.531A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.517A 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 248 removed outlier: 3.689A 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 265 through 268 removed outlier: 4.072A pdb=" N GLY E 268 " --> pdb=" O HIS E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 268' Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 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: 4.172A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 414 removed outlier: 3.515A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (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 448 through 466 removed outlier: 4.416A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) 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 484 removed outlier: 3.568A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) 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 534 removed outlier: 4.367A 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 559 removed outlier: 3.883A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (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 303 Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.992A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 372 removed outlier: 4.358A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.668A pdb=" N ASP F 389 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 removed outlier: 4.304A pdb=" N ARG F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.544A pdb=" N GLU F 619 " --> pdb=" O ASN F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 756 removed outlier: 3.791A 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 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 891 removed outlier: 4.154A pdb=" N GLY F 891 " --> pdb=" O PHE F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 910 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.301A 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 968 removed outlier: 3.687A pdb=" N GLN F 949 " --> pdb=" O LEU F 945 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 966 " --> pdb=" O LEU F 962 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER F 967 " --> pdb=" O VAL F 963 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 968 " --> pdb=" O LYS F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.444A 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: 5.565A 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 352 removed outlier: 5.902A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.523A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.353A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.137A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.800A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.884A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.344A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.578A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.329A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.030A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.583A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 347 through 352 removed outlier: 5.855A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 28 through 30 removed outlier: 5.281A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 95 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 188 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AC7, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.081A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 84 through 85 removed outlier: 5.887A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 311 through 319 removed outlier: 6.870A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.549A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.106A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.475A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.475A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'D' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'D' and resid 1086 through 1090 removed outlier: 4.392A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AE3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.391A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 347 through 352 removed outlier: 5.790A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 28 through 30 removed outlier: 8.694A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 48 through 55 removed outlier: 3.849A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 83 through 85 removed outlier: 4.078A pdb=" N LEU F 141 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 83 through 85 removed outlier: 6.371A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 311 through 319 removed outlier: 6.806A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AF2, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AF3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'F' and resid 654 through 660 removed outlier: 4.758A pdb=" N THR F 696 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN F 658 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN F 717 " --> pdb=" O ALA F1070 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN F 717 " --> pdb=" O ALA F1070 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.246A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.353A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 1094 through 1097 1889 hydrogen bonds defined for protein. 5346 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: 8.87 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12420 1.34 - 1.46: 9797 1.46 - 1.58: 17242 1.58 - 1.70: 0 1.70 - 1.82: 267 Bond restraints: 39726 Sorted by residual: bond pdb=" C1 NAG F1307 " pdb=" O5 NAG F1307 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 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 I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 39721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 53329 1.97 - 3.94: 652 3.94 - 5.92: 67 5.92 - 7.89: 3 7.89 - 9.86: 2 Bond angle restraints: 54053 Sorted by residual: angle pdb=" C PRO D 807 " pdb=" N ASP D 808 " pdb=" CA ASP D 808 " ideal model delta sigma weight residual 122.31 112.45 9.86 2.34e+00 1.83e-01 1.78e+01 angle pdb=" N GLY B 857 " pdb=" CA GLY B 857 " pdb=" C GLY B 857 " ideal model delta sigma weight residual 113.58 110.18 3.40 1.07e+00 8.73e-01 1.01e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 111.88 108.56 3.32 1.06e+00 8.90e-01 9.80e+00 angle pdb=" N ILE C 259 " pdb=" CA ILE C 259 " pdb=" C ILE C 259 " ideal model delta sigma weight residual 111.81 109.17 2.64 8.60e-01 1.35e+00 9.40e+00 angle pdb=" C ASN A 194 " pdb=" N HIS A 195 " pdb=" CA HIS A 195 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.97e+00 ... (remaining 54048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.99: 23226 24.99 - 49.99: 779 49.99 - 74.98: 139 74.98 - 99.97: 44 99.97 - 124.97: 70 Dihedral angle restraints: 24258 sinusoidal: 10223 harmonic: 14035 Sorted by residual: dihedral pdb=" C2 NAG B1307 " pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " pdb=" C5 NAG B1307 " ideal model delta sinusoidal sigma weight residual -62.96 62.01 -124.97 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sinusoidal sigma weight residual -62.96 56.35 -119.31 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 NAG R 1 " pdb=" C5 NAG R 1 " pdb=" O5 NAG R 1 " pdb=" C4 NAG R 1 " ideal model delta sinusoidal sigma weight residual -64.11 53.78 -117.89 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 24255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 6034 0.111 - 0.223: 83 0.223 - 0.334: 4 0.334 - 0.445: 2 0.445 - 0.557: 2 Chirality restraints: 6125 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 125 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 6122 not shown) Planarity restraints: 6974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 891 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 892 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 892 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 892 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 527 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 987 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.022 5.00e-02 4.00e+02 ... (remaining 6971 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1371 2.70 - 3.25: 42348 3.25 - 3.80: 70023 3.80 - 4.35: 86038 4.35 - 4.90: 138845 Nonbonded interactions: 338625 Sorted by model distance: nonbonded pdb=" OG1 THR D 478 " pdb=" O PHE D 486 " model vdw 2.151 3.040 nonbonded pdb=" O GLU D 661 " pdb=" OH TYR D 695 " model vdw 2.163 3.040 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.163 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.165 3.040 nonbonded pdb=" O4 NAG B1309 " pdb=" O7 NAG B1309 " model vdw 2.168 3.040 ... (remaining 338620 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 78 or (resid 79 through 80 and (name N or name \ CA or name C or name O or name CB )) or resid 81 through 189 or (resid 190 throu \ gh 191 and (name N or name CA or name C or name O or name CB )) or resid 192 thr \ ough 248 or resid 251 through 269 or (resid 270 and (name N or name CA or name C \ or name O or name CB )) or resid 271 through 296 or (resid 297 and (name N or n \ ame CA or name C or name O or name CB )) or resid 298 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 4 or (resid 465 and (name N or name CA or name C or name O or name CB )) or resi \ d 466 through 615)) selection = (chain 'C' and (resid 19 through 78 or (resid 79 through 80 and (name N or name \ CA or name C or name O or name CB )) or resid 81 through 248 or resid 251 throug \ h 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or \ resid 271 through 296 or (resid 297 and (name N or name CA or name C or name O o \ r name CB )) or resid 298 through 615)) selection = (chain 'E' and (resid 19 through 189 or (resid 190 through 191 and (name N or na \ me CA or name C or name O or name CB )) or resid 192 through 615)) } ncs_group { reference = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 or (resid 200 and (name N \ or name CA or name C or name O or name CB )) or resid 201 through 354 or (resid \ 355 and (name N or name CA or name C or name O or name CB )) or resid 356 throug \ h 485 or (resid 486 and (name N or name CA or name C or name O or name CB )) or \ resid 487 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 579 or (resid 580 and (name N or name CA or na \ me C or name O or name CB )) or resid 581 through 883 or (resid 884 and (name N \ or name CA or name C or name O or name CB )) or resid 885 through 911 or (resid \ 912 and (name N or name CA or name C or name O or name CB )) or resid 913 throug \ h 949 or (resid 950 and (name N or name CA or name C or name O or name CB )) or \ resid 951 through 1040 or (resid 1041 and (name N or name CA or name C or name O \ or name CB )) or resid 1042 through 1100 or (resid 1101 and (name N or name CA \ or name C or name O or name CB )) or resid 1102 through 1144 or resid 1302 throu \ gh 1308)) selection = (chain 'D' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 48 \ 5 or (resid 486 and (name N or name CA or name C or name O or name CB )) or resi \ d 487 through 579 or (resid 580 and (name N or name CA or name C or name O or na \ me CB )) or resid 581 through 710 or (resid 711 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 n \ ame CA or name C or name O or name CB )) or resid 913 through 949 or (resid 950 \ and (name N or name CA or name C or name O or name CB )) or resid 951 through 11 \ 44 or resid 1301 through 1307)) selection = (chain 'F' and (resid 27 through 197 or (resid 198 and (name N or name CA or nam \ e C or name O or name CB )) or resid 199 through 214 or (resid 215 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 354 or (resid 3 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 356 through \ 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) or r \ esid 529 through 710 or (resid 711 and (name N or name CA or name C or name O or \ name CB )) or resid 712 through 883 or (resid 884 and (name N or name CA or nam \ e C or name O or name CB )) or resid 885 through 1100 or (resid 1101 and (name N \ or name CA or name C or name O or name CB )) or resid 1102 through 1144 or resi \ d 1302 through 1308)) } 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 group one per residue 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.860 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 36.160 Find NCS groups from input model: 1.040 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.003 0.105 39822 Z= 0.166 Angle : 0.555 12.488 54296 Z= 0.278 Chirality : 0.043 0.557 6125 Planarity : 0.003 0.041 6935 Dihedral : 14.828 124.966 15083 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.79 % Allowed : 7.44 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.88 (0.13), residues: 4752 helix: 2.25 (0.13), residues: 1780 sheet: -0.39 (0.18), residues: 747 loop : -0.42 (0.14), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.011 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00333 (39726) covalent geometry : angle 0.53306 (54053) SS BOND : bond 0.00252 ( 45) SS BOND : angle 0.71935 ( 90) hydrogen bonds : bond 0.12447 ( 1854) hydrogen bonds : angle 5.84574 ( 5346) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 1.86926 ( 36) link_NAG-ASN : bond 0.00573 ( 39) link_NAG-ASN : angle 3.15518 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 136 time to evaluate : 1.382 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.5205 (ptt) cc_final: 0.4885 (ptt) REVERT: A 297 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6375 (mpp) REVERT: A 366 MET cc_start: 0.6484 (tpt) cc_final: 0.6169 (tpt) REVERT: A 376 MET cc_start: 0.7952 (ptp) cc_final: 0.7741 (ptp) REVERT: A 474 MET cc_start: 0.5348 (tpt) cc_final: 0.4431 (mmp) REVERT: B 868 GLU cc_start: 0.8934 (mp0) cc_final: 0.8677 (mp0) REVERT: B 1031 GLU cc_start: 0.8554 (tp30) cc_final: 0.8317 (mm-30) REVERT: C 474 MET cc_start: 0.4144 (tpp) cc_final: 0.3635 (tpp) REVERT: D 440 ASN cc_start: 0.9606 (OUTLIER) cc_final: 0.9384 (p0) REVERT: D 780 GLU cc_start: 0.8775 (pt0) cc_final: 0.8441 (pt0) REVERT: D 784 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8479 (mm-40) REVERT: E 332 MET cc_start: 0.7228 (ttp) cc_final: 0.6926 (ttt) REVERT: E 474 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.4101 (tpt) REVERT: F 240 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (p) REVERT: F 1050 MET cc_start: 0.8362 (pmm) cc_final: 0.7934 (pmm) outliers start: 117 outliers final: 54 residues processed: 241 average time/residue: 0.2112 time to fit residues: 89.5368 Evaluate side-chains 171 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 440 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 544 ASN Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 1107 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 6.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 239 GLN B 580 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN D 239 GLN D 394 ASN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 935 GLN D1071 GLN E 81 GLN E 101 GLN E 300 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.072513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046055 restraints weight = 363259.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.045264 restraints weight = 173492.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045329 restraints weight = 103479.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045335 restraints weight = 66537.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.045252 restraints weight = 64720.485| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 39822 Z= 0.255 Angle : 0.660 11.687 54296 Z= 0.325 Chirality : 0.045 0.451 6125 Planarity : 0.004 0.051 6935 Dihedral : 13.678 115.217 6328 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.91 % Allowed : 9.13 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 4752 helix: 1.89 (0.12), residues: 1810 sheet: -0.52 (0.18), residues: 732 loop : -0.43 (0.14), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 177 TYR 0.020 0.002 TYR F 707 PHE 0.019 0.002 PHE E 314 TRP 0.012 0.001 TRP A 165 HIS 0.011 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00523 (39726) covalent geometry : angle 0.64101 (54053) SS BOND : bond 0.00788 ( 45) SS BOND : angle 0.96194 ( 90) hydrogen bonds : bond 0.04166 ( 1854) hydrogen bonds : angle 5.22601 ( 5346) link_BETA1-4 : bond 0.00536 ( 12) link_BETA1-4 : angle 1.89212 ( 36) link_NAG-ASN : bond 0.00575 ( 39) link_NAG-ASN : angle 3.28154 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 119 time to evaluate : 1.519 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.5422 (ptt) cc_final: 0.5088 (ptt) REVERT: A 366 MET cc_start: 0.6294 (tpt) cc_final: 0.5634 (tpt) REVERT: A 376 MET cc_start: 0.8163 (ptp) cc_final: 0.7959 (ptp) REVERT: A 474 MET cc_start: 0.6561 (tpt) cc_final: 0.5919 (mmp) REVERT: B 868 GLU cc_start: 0.9037 (mp0) cc_final: 0.8814 (mp0) REVERT: C 332 MET cc_start: 0.7162 (ppp) cc_final: 0.6886 (ppp) REVERT: C 455 MET cc_start: 0.5896 (ppp) cc_final: 0.5241 (ppp) REVERT: C 474 MET cc_start: 0.6170 (tpp) cc_final: 0.5622 (tpp) REVERT: D 303 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9481 (mm) REVERT: D 560 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8524 (mm) REVERT: D 661 GLU cc_start: 0.8662 (tp30) cc_final: 0.8356 (tm-30) REVERT: D 784 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8736 (mm-40) REVERT: E 455 MET cc_start: 0.1912 (ppp) cc_final: 0.1426 (ppp) REVERT: E 480 MET cc_start: 0.7843 (ptt) cc_final: 0.7484 (ppp) REVERT: F 560 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8373 (mm) REVERT: F 577 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8950 (ptm160) outliers start: 122 outliers final: 71 residues processed: 228 average time/residue: 0.2224 time to fit residues: 88.2549 Evaluate side-chains 188 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 113 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 308 optimal weight: 0.8980 chunk 321 optimal weight: 40.0000 chunk 311 optimal weight: 8.9990 chunk 464 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 437 ASN C 58 ASN C 472 GLN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.073658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.047659 restraints weight = 358801.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.047909 restraints weight = 174328.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047899 restraints weight = 97051.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.047994 restraints weight = 85164.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048142 restraints weight = 80084.584| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39822 Z= 0.125 Angle : 0.586 12.910 54296 Z= 0.282 Chirality : 0.045 0.485 6125 Planarity : 0.004 0.119 6935 Dihedral : 11.615 112.649 6300 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.41 % Allowed : 10.23 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 4752 helix: 2.00 (0.12), residues: 1804 sheet: -0.40 (0.18), residues: 737 loop : -0.41 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 577 TYR 0.017 0.001 TYR E 385 PHE 0.034 0.001 PHE E 314 TRP 0.013 0.001 TRP A 165 HIS 0.009 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00265 (39726) covalent geometry : angle 0.56341 (54053) SS BOND : bond 0.00262 ( 45) SS BOND : angle 0.78479 ( 90) hydrogen bonds : bond 0.03561 ( 1854) hydrogen bonds : angle 4.94717 ( 5346) link_BETA1-4 : bond 0.00593 ( 12) link_BETA1-4 : angle 2.01227 ( 36) link_NAG-ASN : bond 0.00579 ( 39) link_NAG-ASN : angle 3.33998 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 123 time to evaluate : 1.572 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8014 (ppp) cc_final: 0.7733 (ppp) REVERT: A 123 MET cc_start: 0.4636 (ptt) cc_final: 0.4326 (ptt) REVERT: A 297 MET cc_start: 0.6682 (mtt) cc_final: 0.6459 (mpp) REVERT: A 366 MET cc_start: 0.6183 (tpt) cc_final: 0.5792 (tpt) REVERT: A 383 MET cc_start: 0.8720 (ptp) cc_final: 0.8047 (ppp) REVERT: A 474 MET cc_start: 0.6432 (tpt) cc_final: 0.5653 (mmp) REVERT: B 697 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8337 (tmm) REVERT: B 868 GLU cc_start: 0.9076 (mp0) cc_final: 0.8777 (mp0) REVERT: B 913 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: B 1050 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8382 (ptp) REVERT: C 474 MET cc_start: 0.4663 (tpp) cc_final: 0.4085 (tpp) REVERT: D 697 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8062 (ptp) REVERT: D 780 GLU cc_start: 0.8822 (pt0) cc_final: 0.8436 (pt0) REVERT: D 784 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8703 (mm-40) REVERT: E 455 MET cc_start: 0.2452 (ppp) cc_final: 0.2058 (ppp) REVERT: E 474 MET cc_start: 0.4130 (tpt) cc_final: 0.3930 (tpt) REVERT: E 480 MET cc_start: 0.7728 (ptt) cc_final: 0.7373 (ppp) REVERT: F 577 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8811 (ptm160) REVERT: F 740 MET cc_start: 0.9045 (ttm) cc_final: 0.8436 (ttt) REVERT: F 1113 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8639 (mp10) outliers start: 101 outliers final: 60 residues processed: 212 average time/residue: 0.2206 time to fit residues: 81.8298 Evaluate side-chains 181 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 115 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1113 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 378 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 chunk 424 optimal weight: 9.9990 chunk 435 optimal weight: 2.9990 chunk 447 optimal weight: 0.7980 chunk 3 optimal weight: 50.0000 chunk 8 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 247 optimal weight: 6.9990 chunk 174 optimal weight: 40.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 101 GLN ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** 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 = 0.3992 r_free = 0.3992 target = 0.073037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.046180 restraints weight = 359517.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 116)---------------| | r_work = 0.3290 r_free = 0.3290 target = 0.044105 restraints weight = 161853.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.044430 restraints weight = 99002.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.044567 restraints weight = 72238.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.044683 restraints weight = 62384.891| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 39822 Z= 0.164 Angle : 0.592 12.950 54296 Z= 0.286 Chirality : 0.044 0.530 6125 Planarity : 0.004 0.049 6935 Dihedral : 10.310 111.611 6295 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.72 % Allowed : 10.59 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.73 (0.12), residues: 4752 helix: 1.98 (0.12), residues: 1805 sheet: -0.44 (0.18), residues: 744 loop : -0.40 (0.14), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.015 0.001 TYR C 385 PHE 0.030 0.001 PHE E 315 TRP 0.013 0.001 TRP A 165 HIS 0.007 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00344 (39726) covalent geometry : angle 0.56702 (54053) SS BOND : bond 0.00646 ( 45) SS BOND : angle 1.09980 ( 90) hydrogen bonds : bond 0.03500 ( 1854) hydrogen bonds : angle 4.92289 ( 5346) link_BETA1-4 : bond 0.00552 ( 12) link_BETA1-4 : angle 2.25602 ( 36) link_NAG-ASN : bond 0.00569 ( 39) link_NAG-ASN : angle 3.37260 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 118 time to evaluate : 1.656 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8103 (ppp) cc_final: 0.7867 (ppp) REVERT: A 123 MET cc_start: 0.5496 (ptt) cc_final: 0.5185 (ptt) REVERT: A 297 MET cc_start: 0.6920 (mtt) cc_final: 0.6542 (mpp) REVERT: A 366 MET cc_start: 0.6213 (tpt) cc_final: 0.5847 (tpt) REVERT: A 462 MET cc_start: 0.7190 (ptt) cc_final: 0.6944 (ptt) REVERT: A 474 MET cc_start: 0.6702 (tpt) cc_final: 0.6063 (mmp) REVERT: A 480 MET cc_start: 0.7361 (ptt) cc_final: 0.6928 (ppp) REVERT: B 697 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8113 (tmm) REVERT: B 868 GLU cc_start: 0.9050 (mp0) cc_final: 0.8758 (mp0) REVERT: B 913 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: B 1050 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8382 (ptp) REVERT: C 474 MET cc_start: 0.7294 (tpp) cc_final: 0.6904 (tpp) REVERT: D 560 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8573 (mm) REVERT: D 697 MET cc_start: 0.8550 (ptp) cc_final: 0.8137 (ptp) REVERT: D 780 GLU cc_start: 0.8760 (pt0) cc_final: 0.8448 (pt0) REVERT: D 784 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8754 (mm-40) REVERT: D 823 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: E 318 VAL cc_start: 0.5742 (OUTLIER) cc_final: 0.5474 (p) REVERT: E 455 MET cc_start: 0.1738 (ppp) cc_final: 0.1377 (ppp) REVERT: E 480 MET cc_start: 0.7821 (ptt) cc_final: 0.7522 (ppp) REVERT: F 226 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8694 (mm) REVERT: F 577 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8959 (ptm160) REVERT: F 697 MET cc_start: 0.8938 (mmm) cc_final: 0.8658 (tpt) outliers start: 114 outliers final: 80 residues processed: 220 average time/residue: 0.2225 time to fit residues: 85.1984 Evaluate side-chains 202 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 114 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 134 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 356 optimal weight: 50.0000 chunk 348 optimal weight: 7.9990 chunk 441 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.072762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.046280 restraints weight = 357752.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.046990 restraints weight = 169029.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046631 restraints weight = 91172.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.046626 restraints weight = 89413.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.046788 restraints weight = 80743.266| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 39822 Z= 0.172 Angle : 0.592 13.337 54296 Z= 0.286 Chirality : 0.044 0.550 6125 Planarity : 0.004 0.049 6935 Dihedral : 9.670 110.111 6295 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.84 % Allowed : 11.59 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.72 (0.12), residues: 4752 helix: 2.00 (0.12), residues: 1805 sheet: -0.47 (0.18), residues: 724 loop : -0.42 (0.14), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.015 0.001 TYR C 385 PHE 0.026 0.001 PHE E 315 TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00359 (39726) covalent geometry : angle 0.56604 (54053) SS BOND : bond 0.00326 ( 45) SS BOND : angle 0.98270 ( 90) hydrogen bonds : bond 0.03458 ( 1854) hydrogen bonds : angle 4.89631 ( 5346) link_BETA1-4 : bond 0.00500 ( 12) link_BETA1-4 : angle 2.49190 ( 36) link_NAG-ASN : bond 0.00574 ( 39) link_NAG-ASN : angle 3.43496 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 116 time to evaluate : 1.620 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8118 (ppp) cc_final: 0.7864 (ppp) REVERT: A 123 MET cc_start: 0.5608 (ptt) cc_final: 0.5295 (ptt) REVERT: A 297 MET cc_start: 0.7026 (mtt) cc_final: 0.6627 (mpp) REVERT: A 366 MET cc_start: 0.6177 (tpt) cc_final: 0.5792 (tpt) REVERT: A 376 MET cc_start: 0.7676 (ptp) cc_final: 0.7470 (ptp) REVERT: A 383 MET cc_start: 0.8941 (ptp) cc_final: 0.8667 (mpp) REVERT: A 474 MET cc_start: 0.6681 (tpt) cc_final: 0.6067 (mmp) REVERT: A 480 MET cc_start: 0.7361 (ptt) cc_final: 0.7105 (ppp) REVERT: B 697 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8300 (tmm) REVERT: B 913 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: B 1050 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8448 (ptp) REVERT: C 455 MET cc_start: 0.6258 (ppp) cc_final: 0.5746 (ppp) REVERT: C 474 MET cc_start: 0.5818 (tpp) cc_final: 0.5225 (tpp) REVERT: D 303 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9426 (mm) REVERT: D 516 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8921 (mp0) REVERT: D 560 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8620 (mm) REVERT: D 697 MET cc_start: 0.8686 (ptp) cc_final: 0.8253 (ptp) REVERT: D 780 GLU cc_start: 0.8780 (pt0) cc_final: 0.8483 (pt0) REVERT: D 784 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8759 (mm-40) REVERT: D 823 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: E 318 VAL cc_start: 0.2993 (OUTLIER) cc_final: 0.2547 (p) REVERT: E 480 MET cc_start: 0.7782 (ptt) cc_final: 0.7441 (ppp) REVERT: F 226 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8641 (mm) REVERT: F 902 MET cc_start: 0.9390 (tpp) cc_final: 0.9069 (tpp) REVERT: F 1113 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8666 (mp10) outliers start: 119 outliers final: 88 residues processed: 226 average time/residue: 0.2159 time to fit residues: 85.5330 Evaluate side-chains 209 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 111 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 98 optimal weight: 0.8980 chunk 329 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 467 optimal weight: 4.9990 chunk 434 optimal weight: 8.9990 chunk 112 optimal weight: 0.0570 chunk 110 optimal weight: 0.4980 chunk 257 optimal weight: 0.0770 chunk 207 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 406 optimal weight: 9.9990 overall best weight: 1.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** 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 = 0.4008 r_free = 0.4008 target = 0.073648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.046784 restraints weight = 358024.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.045904 restraints weight = 161419.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046312 restraints weight = 96873.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.046527 restraints weight = 68935.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046187 restraints weight = 59998.253| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 39822 Z= 0.109 Angle : 0.576 13.468 54296 Z= 0.275 Chirality : 0.044 0.540 6125 Planarity : 0.003 0.049 6935 Dihedral : 9.052 108.714 6294 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.43 % Allowed : 12.06 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 4752 helix: 2.03 (0.12), residues: 1808 sheet: -0.33 (0.18), residues: 738 loop : -0.36 (0.14), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 177 TYR 0.018 0.001 TYR C 385 PHE 0.023 0.001 PHE E 315 TRP 0.014 0.001 TRP A 165 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00229 (39726) covalent geometry : angle 0.55085 (54053) SS BOND : bond 0.00251 ( 45) SS BOND : angle 0.80667 ( 90) hydrogen bonds : bond 0.03240 ( 1854) hydrogen bonds : angle 4.75712 ( 5346) link_BETA1-4 : bond 0.00768 ( 12) link_BETA1-4 : angle 2.27889 ( 36) link_NAG-ASN : bond 0.00626 ( 39) link_NAG-ASN : angle 3.45628 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 121 time to evaluate : 1.582 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8146 (ppp) cc_final: 0.7896 (ppp) REVERT: A 123 MET cc_start: 0.5415 (ptt) cc_final: 0.2070 (ttt) REVERT: A 297 MET cc_start: 0.6933 (mtt) cc_final: 0.6500 (mpp) REVERT: A 366 MET cc_start: 0.6155 (tpt) cc_final: 0.5746 (tpt) REVERT: A 474 MET cc_start: 0.6519 (tpt) cc_final: 0.5937 (mmp) REVERT: A 480 MET cc_start: 0.7250 (ptt) cc_final: 0.6958 (ppp) REVERT: B 294 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8230 (p0) REVERT: B 697 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8246 (tmm) REVERT: B 913 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: B 1050 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8324 (ptp) REVERT: B 1066 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (m) REVERT: C 474 MET cc_start: 0.7254 (tpp) cc_final: 0.6887 (tpp) REVERT: D 516 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8909 (pp20) REVERT: D 560 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8606 (mm) REVERT: D 697 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8226 (ptp) REVERT: D 780 GLU cc_start: 0.8702 (pt0) cc_final: 0.8398 (pt0) REVERT: D 781 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9066 (p) REVERT: D 784 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8716 (mm-40) REVERT: D 823 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: E 455 MET cc_start: 0.1820 (ppp) cc_final: 0.1475 (ppp) REVERT: E 480 MET cc_start: 0.7730 (ptt) cc_final: 0.7408 (ppp) REVERT: F 226 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8773 (mm) REVERT: F 697 MET cc_start: 0.8719 (mmm) cc_final: 0.8418 (tpp) REVERT: F 902 MET cc_start: 0.9296 (tpp) cc_final: 0.9018 (tpp) REVERT: F 1031 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8363 (tm-30) REVERT: F 1113 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (mp10) outliers start: 102 outliers final: 63 residues processed: 212 average time/residue: 0.1973 time to fit residues: 72.9949 Evaluate side-chains 188 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 113 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 77 optimal weight: 9.9990 chunk 359 optimal weight: 40.0000 chunk 218 optimal weight: 0.0170 chunk 29 optimal weight: 50.0000 chunk 212 optimal weight: 9.9990 chunk 187 optimal weight: 0.1980 chunk 377 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 313 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 overall best weight: 4.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.072588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046082 restraints weight = 361292.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045801 restraints weight = 172549.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.045828 restraints weight = 131839.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.046206 restraints weight = 83036.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045970 restraints weight = 57749.837| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 39822 Z= 0.186 Angle : 0.612 13.736 54296 Z= 0.296 Chirality : 0.044 0.577 6125 Planarity : 0.004 0.049 6935 Dihedral : 8.760 107.458 6282 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.60 % Allowed : 12.35 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4752 helix: 2.01 (0.12), residues: 1809 sheet: -0.39 (0.18), residues: 716 loop : -0.37 (0.14), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.015 0.001 TYR C 385 PHE 0.023 0.001 PHE E 315 TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00389 (39726) covalent geometry : angle 0.58682 (54053) SS BOND : bond 0.00354 ( 45) SS BOND : angle 0.82835 ( 90) hydrogen bonds : bond 0.03416 ( 1854) hydrogen bonds : angle 4.84049 ( 5346) link_BETA1-4 : bond 0.00584 ( 12) link_BETA1-4 : angle 2.04737 ( 36) link_NAG-ASN : bond 0.00602 ( 39) link_NAG-ASN : angle 3.60671 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 117 time to evaluate : 1.342 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.5514 (ptt) cc_final: 0.2232 (ttt) REVERT: A 366 MET cc_start: 0.6229 (tpt) cc_final: 0.5616 (tpt) REVERT: A 474 MET cc_start: 0.6543 (tpt) cc_final: 0.5983 (mmp) REVERT: A 480 MET cc_start: 0.7259 (ptt) cc_final: 0.6974 (ppp) REVERT: B 294 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 697 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: C 474 MET cc_start: 0.6077 (tpp) cc_final: 0.5534 (tpp) REVERT: D 303 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9453 (mm) REVERT: D 560 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8687 (mm) REVERT: D 697 MET cc_start: 0.8756 (ptp) cc_final: 0.8298 (ptp) REVERT: D 780 GLU cc_start: 0.8739 (pt0) cc_final: 0.8438 (pt0) REVERT: D 784 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8777 (mm-40) REVERT: D 823 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.9034 (m-80) REVERT: E 152 MET cc_start: 0.1227 (ptm) cc_final: 0.0780 (ptm) REVERT: E 455 MET cc_start: 0.1813 (ppp) cc_final: 0.1416 (ppp) REVERT: E 480 MET cc_start: 0.7707 (ptt) cc_final: 0.7402 (ppp) REVERT: F 226 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8728 (mm) REVERT: F 697 MET cc_start: 0.8743 (tmm) cc_final: 0.8491 (tpp) REVERT: F 869 MET cc_start: 0.9194 (ptp) cc_final: 0.8973 (ptm) outliers start: 109 outliers final: 82 residues processed: 215 average time/residue: 0.2163 time to fit residues: 82.0005 Evaluate side-chains 200 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 112 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 129 optimal weight: 0.0170 chunk 169 optimal weight: 50.0000 chunk 342 optimal weight: 0.6980 chunk 264 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 472 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 overall best weight: 2.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.073084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.046304 restraints weight = 357997.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.044410 restraints weight = 161862.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.044785 restraints weight = 98833.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.044946 restraints weight = 72886.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.045005 restraints weight = 62592.254| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39822 Z= 0.133 Angle : 0.601 14.054 54296 Z= 0.287 Chirality : 0.044 0.564 6125 Planarity : 0.004 0.049 6935 Dihedral : 8.485 106.453 6282 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.27 % Allowed : 12.80 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 4752 helix: 2.01 (0.12), residues: 1807 sheet: -0.37 (0.18), residues: 724 loop : -0.37 (0.14), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 328 TYR 0.017 0.001 TYR C 385 PHE 0.049 0.001 PHE D 490 TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00279 (39726) covalent geometry : angle 0.57475 (54053) SS BOND : bond 0.00292 ( 45) SS BOND : angle 0.77898 ( 90) hydrogen bonds : bond 0.03306 ( 1854) hydrogen bonds : angle 4.81406 ( 5346) link_BETA1-4 : bond 0.00599 ( 12) link_BETA1-4 : angle 2.06938 ( 36) link_NAG-ASN : bond 0.00591 ( 39) link_NAG-ASN : angle 3.61824 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 117 time to evaluate : 1.288 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8135 (ptp) cc_final: 0.7431 (ppp) REVERT: A 123 MET cc_start: 0.5526 (ptt) cc_final: 0.1699 (ttt) REVERT: A 366 MET cc_start: 0.6122 (tpt) cc_final: 0.5588 (tpt) REVERT: A 474 MET cc_start: 0.6501 (tpt) cc_final: 0.5986 (mmp) REVERT: A 480 MET cc_start: 0.7238 (ptt) cc_final: 0.6937 (ppp) REVERT: B 294 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8122 (p0) REVERT: B 697 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: B 1031 GLU cc_start: 0.8703 (tp30) cc_final: 0.8114 (mm-30) REVERT: C 474 MET cc_start: 0.7151 (tpp) cc_final: 0.6764 (tpp) REVERT: D 560 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8648 (mm) REVERT: D 697 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8227 (ptp) REVERT: D 780 GLU cc_start: 0.8712 (pt0) cc_final: 0.8433 (pt0) REVERT: D 781 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9100 (p) REVERT: D 784 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8756 (mm-40) REVERT: D 823 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.9013 (m-80) REVERT: E 480 MET cc_start: 0.7728 (ptt) cc_final: 0.7378 (ppp) REVERT: F 226 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8730 (mm) REVERT: F 1031 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8540 (tm-30) outliers start: 95 outliers final: 75 residues processed: 201 average time/residue: 0.2216 time to fit residues: 78.0519 Evaluate side-chains 196 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 114 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 455 optimal weight: 0.7980 chunk 3 optimal weight: 50.0000 chunk 359 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 15 optimal weight: 50.0000 chunk 382 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 472 GLN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.072601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.045634 restraints weight = 360836.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.044719 restraints weight = 163428.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.044856 restraints weight = 98364.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.044898 restraints weight = 74704.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.044998 restraints weight = 65487.468| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39822 Z= 0.174 Angle : 0.627 14.268 54296 Z= 0.302 Chirality : 0.044 0.582 6125 Planarity : 0.004 0.048 6935 Dihedral : 8.350 105.660 6282 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.41 % Allowed : 12.80 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.73 (0.12), residues: 4752 helix: 1.97 (0.12), residues: 1807 sheet: -0.45 (0.18), residues: 721 loop : -0.39 (0.14), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.016 0.001 TYR C 385 PHE 0.023 0.001 PHE E 315 TRP 0.013 0.001 TRP A 165 HIS 0.008 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00364 (39726) covalent geometry : angle 0.60162 (54053) SS BOND : bond 0.00354 ( 45) SS BOND : angle 0.80288 ( 90) hydrogen bonds : bond 0.03432 ( 1854) hydrogen bonds : angle 4.88102 ( 5346) link_BETA1-4 : bond 0.00558 ( 12) link_BETA1-4 : angle 2.01007 ( 36) link_NAG-ASN : bond 0.00597 ( 39) link_NAG-ASN : angle 3.63647 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 115 time to evaluate : 1.507 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8287 (ptp) cc_final: 0.7595 (ppp) REVERT: A 123 MET cc_start: 0.4847 (ptt) cc_final: 0.4562 (ptt) REVERT: A 297 MET cc_start: 0.7181 (mtt) cc_final: 0.6878 (mpp) REVERT: A 366 MET cc_start: 0.6082 (tpt) cc_final: 0.5691 (tpt) REVERT: A 474 MET cc_start: 0.6491 (tpt) cc_final: 0.5973 (mmp) REVERT: A 480 MET cc_start: 0.7205 (ptt) cc_final: 0.6906 (ppp) REVERT: B 294 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 697 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8212 (tmm) REVERT: B 1031 GLU cc_start: 0.8689 (tp30) cc_final: 0.8118 (mm-30) REVERT: C 332 MET cc_start: 0.8212 (ptm) cc_final: 0.7893 (ppp) REVERT: C 360 MET cc_start: 0.6643 (mmm) cc_final: 0.6194 (mmm) REVERT: C 474 MET cc_start: 0.7037 (tpp) cc_final: 0.6653 (tpp) REVERT: D 560 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8714 (mm) REVERT: D 697 MET cc_start: 0.8725 (ptp) cc_final: 0.8272 (ptp) REVERT: D 740 MET cc_start: 0.9368 (ttm) cc_final: 0.9123 (tmm) REVERT: D 780 GLU cc_start: 0.8741 (pt0) cc_final: 0.8448 (pt0) REVERT: D 784 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8769 (mm-40) REVERT: D 823 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.9047 (m-80) REVERT: E 455 MET cc_start: 0.1846 (ppp) cc_final: 0.1381 (ppp) REVERT: E 480 MET cc_start: 0.7708 (ptt) cc_final: 0.7350 (ppp) REVERT: F 226 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8740 (mm) REVERT: F 1031 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8215 (tm-30) outliers start: 101 outliers final: 85 residues processed: 204 average time/residue: 0.2066 time to fit residues: 73.9627 Evaluate side-chains 205 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 115 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 211 optimal weight: 40.0000 chunk 331 optimal weight: 40.0000 chunk 328 optimal weight: 50.0000 chunk 314 optimal weight: 5.9990 chunk 29 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 268 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 386 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS C 472 GLN ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN E 210 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.072328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.045717 restraints weight = 358786.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.043722 restraints weight = 166693.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.043855 restraints weight = 102192.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.043987 restraints weight = 73763.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.044114 restraints weight = 63957.375| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 39822 Z= 0.185 Angle : 0.642 15.259 54296 Z= 0.310 Chirality : 0.044 0.587 6125 Planarity : 0.004 0.048 6935 Dihedral : 8.265 105.668 6282 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 13.02 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.68 (0.12), residues: 4752 helix: 1.93 (0.12), residues: 1808 sheet: -0.46 (0.18), residues: 714 loop : -0.43 (0.14), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 355 TYR 0.025 0.001 TYR B 396 PHE 0.035 0.001 PHE D 490 TRP 0.012 0.001 TRP A 165 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (39726) covalent geometry : angle 0.61775 (54053) SS BOND : bond 0.00362 ( 45) SS BOND : angle 0.84835 ( 90) hydrogen bonds : bond 0.03497 ( 1854) hydrogen bonds : angle 4.91395 ( 5346) link_BETA1-4 : bond 0.00537 ( 12) link_BETA1-4 : angle 2.00957 ( 36) link_NAG-ASN : bond 0.00580 ( 39) link_NAG-ASN : angle 3.63341 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 116 time to evaluate : 1.700 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8282 (ptp) cc_final: 0.7604 (ppp) REVERT: A 123 MET cc_start: 0.5122 (ptt) cc_final: 0.4823 (ptt) REVERT: A 297 MET cc_start: 0.7247 (mtt) cc_final: 0.6962 (mpp) REVERT: A 366 MET cc_start: 0.6097 (tpt) cc_final: 0.5648 (tpt) REVERT: A 474 MET cc_start: 0.6464 (tpt) cc_final: 0.5939 (mmp) REVERT: A 480 MET cc_start: 0.7163 (ptt) cc_final: 0.6875 (ppp) REVERT: B 118 LEU cc_start: 0.9553 (tt) cc_final: 0.9082 (mt) REVERT: B 294 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8138 (p0) REVERT: B 697 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8237 (tmm) REVERT: C 332 MET cc_start: 0.7448 (ptm) cc_final: 0.6902 (ppp) REVERT: C 360 MET cc_start: 0.7133 (mmm) cc_final: 0.6662 (mmt) REVERT: C 474 MET cc_start: 0.6596 (tpp) cc_final: 0.6187 (tpp) REVERT: D 560 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8727 (mm) REVERT: D 697 MET cc_start: 0.8779 (ptp) cc_final: 0.8323 (ptp) REVERT: D 784 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8994 (tp40) REVERT: E 455 MET cc_start: 0.1816 (ppp) cc_final: 0.1370 (ppp) REVERT: E 480 MET cc_start: 0.7718 (ptt) cc_final: 0.7374 (ppp) REVERT: F 226 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8766 (mm) REVERT: F 1029 MET cc_start: 0.9072 (tpp) cc_final: 0.8849 (mmm) REVERT: F 1031 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8273 (tm-30) outliers start: 95 outliers final: 81 residues processed: 203 average time/residue: 0.2192 time to fit residues: 78.9338 Evaluate side-chains 199 residues out of total 4226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 114 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 781 VAL Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1019 ARG Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1066 THR Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 738 CYS Chi-restraints excluded: chain F residue 786 LYS Chi-restraints excluded: chain F residue 794 ILE Chi-restraints excluded: chain F residue 883 THR Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1066 THR Chi-restraints excluded: chain F residue 1103 PHE Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1107 ARG Chi-restraints excluded: chain F residue 1123 SER Chi-restraints excluded: chain F residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 260 optimal weight: 9.9990 chunk 329 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 43 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 108 optimal weight: 0.1980 chunk 201 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 556 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.072002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045567 restraints weight = 362836.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045560 restraints weight = 171823.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.045127 restraints weight = 98705.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045495 restraints weight = 83276.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045192 restraints weight = 67047.910| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 39822 Z= 0.207 Angle : 0.654 13.150 54296 Z= 0.317 Chirality : 0.044 0.596 6125 Planarity : 0.004 0.048 6935 Dihedral : 8.197 105.869 6278 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.27 % Allowed : 13.02 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4752 helix: 1.87 (0.12), residues: 1808 sheet: -0.52 (0.18), residues: 699 loop : -0.45 (0.14), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 815 TYR 0.022 0.001 TYR B 396 PHE 0.036 0.001 PHE D 490 TRP 0.013 0.001 TRP C 168 HIS 0.011 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00430 (39726) covalent geometry : angle 0.63029 (54053) SS BOND : bond 0.00403 ( 45) SS BOND : angle 0.91099 ( 90) hydrogen bonds : bond 0.03578 ( 1854) hydrogen bonds : angle 4.99236 ( 5346) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 2.01078 ( 36) link_NAG-ASN : bond 0.00567 ( 39) link_NAG-ASN : angle 3.63306 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14442.74 seconds wall clock time: 247 minutes 16.06 seconds (14836.06 seconds total)