Starting phenix.real_space_refine on Sat Feb 24 19:26:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc9_28977/02_2024/8fc9_28977_trim.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5096 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 13892 2.51 5 N 3836 2.21 5 O 3968 1.98 5 H 19312 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 7676 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 17, 'TRANS': 565} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 341 Chain: "E" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "F" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 7676 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 17, 'TRANS': 565} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 341 Chain: "C" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 7676 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 17, 'TRANS': 565} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 341 Chain: "D" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 7676 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 17, 'TRANS': 565} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 341 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.68, per 1000 atoms: 0.45 Number of scatterers: 41124 At special positions: 0 Unit cell: (201.96, 200.88, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 104 16.00 P 8 15.00 Mg 4 11.99 O 3968 8.00 N 3836 7.00 C 13892 6.00 H 19312 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.70 Conformation dependent library (CDL) restraints added in 4.8 seconds 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 12 sheets defined 65.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.594A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.412A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.547A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.555A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.701A pdb=" N ASN A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.769A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.626A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 487 removed outlier: 3.932A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.875A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.767A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 removed outlier: 3.593A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.906A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.574A pdb=" N PHE A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.927A pdb=" N SER A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 688' Processing helix chain 'A' and resid 691 through 720 removed outlier: 3.540A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 748 removed outlier: 3.916A pdb=" N VAL A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 removed outlier: 3.831A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 28 Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.863A pdb=" N LEU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 89 through 98 removed outlier: 4.092A pdb=" N GLU E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Proline residue: E 96 - end of helix No H-bonds generated for 'chain 'E' and resid 89 through 98' Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.654A pdb=" N GLU E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.547A pdb=" N ARG E 122 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.884A pdb=" N MET E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'E' and resid 166 through 180 removed outlier: 3.691A pdb=" N GLN E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 28 Processing helix chain 'F' and resid 65 through 70 removed outlier: 3.863A pdb=" N LEU F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 89 through 98 removed outlier: 4.092A pdb=" N GLU F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) Proline residue: F 96 - end of helix No H-bonds generated for 'chain 'F' and resid 89 through 98' Processing helix chain 'F' and resid 98 through 107 removed outlier: 3.653A pdb=" N GLU F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.547A pdb=" N ARG F 122 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.885A pdb=" N MET F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.691A pdb=" N GLN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 28 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.862A pdb=" N LEU G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 74 Processing helix chain 'G' and resid 89 through 98 removed outlier: 4.091A pdb=" N GLU G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Proline residue: G 96 - end of helix No H-bonds generated for 'chain 'G' and resid 89 through 98' Processing helix chain 'G' and resid 98 through 107 removed outlier: 3.654A pdb=" N GLU G 102 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.547A pdb=" N ARG G 122 " --> pdb=" O LYS G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.884A pdb=" N MET G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 151 Processing helix chain 'G' and resid 166 through 180 removed outlier: 3.692A pdb=" N GLN G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 28 Processing helix chain 'H' and resid 65 through 70 removed outlier: 3.863A pdb=" N LEU H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 Processing helix chain 'H' and resid 89 through 98 removed outlier: 4.092A pdb=" N GLU H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) Proline residue: H 96 - end of helix No H-bonds generated for 'chain 'H' and resid 89 through 98' Processing helix chain 'H' and resid 98 through 107 removed outlier: 3.654A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 123 removed outlier: 3.547A pdb=" N ARG H 122 " --> pdb=" O LYS H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 134 removed outlier: 3.885A pdb=" N MET H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 151 Processing helix chain 'H' and resid 166 through 180 removed outlier: 3.692A pdb=" N GLN H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.594A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.412A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.546A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.555A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.701A pdb=" N ASN B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.768A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.626A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 487 removed outlier: 3.933A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 Processing helix chain 'B' and resid 550 through 570 removed outlier: 3.875A pdb=" N ILE B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 565 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.768A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 612 removed outlier: 3.592A pdb=" N ILE B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.906A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.574A pdb=" N PHE B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.927A pdb=" N SER B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 683 through 688' Processing helix chain 'B' and resid 691 through 720 removed outlier: 3.540A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 719 " --> pdb=" O ILE B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 748 removed outlier: 3.915A pdb=" N VAL B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 727 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 removed outlier: 3.831A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.594A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.412A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 260 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.547A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.555A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.700A pdb=" N ASN C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.768A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.626A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 487 removed outlier: 3.933A pdb=" N PHE C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 532 Processing helix chain 'C' and resid 550 through 570 removed outlier: 3.874A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA C 565 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.767A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 612 removed outlier: 3.593A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 637 removed outlier: 3.907A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 679 removed outlier: 3.575A pdb=" N PHE C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 688 removed outlier: 3.928A pdb=" N SER C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 683 through 688' Processing helix chain 'C' and resid 691 through 720 removed outlier: 3.540A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 714 " --> pdb=" O LEU C 710 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 719 " --> pdb=" O ILE C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 748 removed outlier: 3.916A pdb=" N VAL C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 removed outlier: 3.831A pdb=" N PHE C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.594A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.411A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.547A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.555A pdb=" N PHE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.701A pdb=" N ASN D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.768A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.626A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 465 " --> pdb=" O ASP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 487 removed outlier: 3.933A pdb=" N PHE D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 532 Processing helix chain 'D' and resid 550 through 570 removed outlier: 3.875A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL D 562 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA D 565 " --> pdb=" O ILE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.767A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 612 removed outlier: 3.592A pdb=" N ILE D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 637 removed outlier: 3.906A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 removed outlier: 3.574A pdb=" N PHE D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 688 removed outlier: 3.927A pdb=" N SER D 687 " --> pdb=" O LEU D 683 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 683 through 688' Processing helix chain 'D' and resid 691 through 720 removed outlier: 3.540A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 719 " --> pdb=" O ILE D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 748 removed outlier: 3.917A pdb=" N VAL D 725 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 727 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 removed outlier: 3.830A pdb=" N PHE D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 410 removed outlier: 3.797A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 760 through 765 removed outlier: 3.559A pdb=" N ARG A 775 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 773 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.407A pdb=" N TYR E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE E 4 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA E 56 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS E 6 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TRP E 58 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 8 " --> pdb=" O TRP E 58 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL E 79 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS E 7 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU E 81 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL E 9 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS E 83 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 11 " --> pdb=" O CYS E 83 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER E 85 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE E 80 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 115 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET E 82 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN E 117 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE E 84 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY E 155 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET E 157 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 42 through 47 removed outlier: 4.408A pdb=" N TYR F 42 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE F 4 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS F 6 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TRP F 58 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU F 8 " --> pdb=" O TRP F 58 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL F 79 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS F 7 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU F 81 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL F 9 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS F 83 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL F 11 " --> pdb=" O CYS F 83 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER F 85 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 80 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET F 82 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN F 117 " --> pdb=" O MET F 82 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE F 84 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY F 155 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET F 157 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 47 removed outlier: 4.406A pdb=" N TYR G 42 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE G 4 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA G 56 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS G 6 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TRP G 58 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU G 8 " --> pdb=" O TRP G 58 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL G 79 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS G 7 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU G 81 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL G 9 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS G 83 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL G 11 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER G 85 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE G 80 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL G 115 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET G 82 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN G 117 " --> pdb=" O MET G 82 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE G 84 " --> pdb=" O ASN G 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY G 155 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET G 157 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 42 through 47 removed outlier: 4.407A pdb=" N TYR H 42 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE H 4 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA H 56 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS H 6 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TRP H 58 " --> pdb=" O LYS H 6 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU H 8 " --> pdb=" O TRP H 58 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL H 79 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS H 7 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU H 81 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL H 9 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS H 83 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL H 11 " --> pdb=" O CYS H 83 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N SER H 85 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE H 80 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL H 115 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET H 82 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN H 117 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE H 84 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY H 155 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET H 157 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 410 removed outlier: 3.797A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 760 through 765 removed outlier: 3.558A pdb=" N ARG B 775 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 773 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.797A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 760 through 765 removed outlier: 3.559A pdb=" N ARG C 775 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP C 773 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.797A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 760 through 765 removed outlier: 3.558A pdb=" N ARG D 775 " --> pdb=" O VAL D 762 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP D 773 " --> pdb=" O VAL D 764 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3579 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: 14.99 Time building geometry restraints manager: 30.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19268 1.03 - 1.23: 47 1.23 - 1.42: 9241 1.42 - 1.62: 12828 1.62 - 1.82: 160 Bond restraints: 41544 Sorted by residual: bond pdb=" NE ARG B 186 " pdb=" HE ARG B 186 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" NE ARG C 186 " pdb=" HE ARG C 186 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" NE ARG A 186 " pdb=" HE ARG A 186 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" NE ARG C 232 " pdb=" HE ARG C 232 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" NE ARG D 186 " pdb=" HE ARG D 186 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 41539 not shown) Histogram of bond angle deviations from ideal: 79.08 - 90.53: 32 90.53 - 101.98: 60 101.98 - 113.43: 47208 113.43 - 124.88: 25137 124.88 - 136.34: 2039 Bond angle restraints: 74476 Sorted by residual: angle pdb="HD21 LEU D 362 " pdb=" CD2 LEU D 362 " pdb="HD23 LEU D 362 " ideal model delta sigma weight residual 110.00 79.79 30.21 3.00e+00 1.11e-01 1.01e+02 angle pdb="HD21 LEU A 362 " pdb=" CD2 LEU A 362 " pdb="HD23 LEU A 362 " ideal model delta sigma weight residual 110.00 79.83 30.17 3.00e+00 1.11e-01 1.01e+02 angle pdb="HD21 LEU C 362 " pdb=" CD2 LEU C 362 " pdb="HD23 LEU C 362 " ideal model delta sigma weight residual 110.00 79.83 30.17 3.00e+00 1.11e-01 1.01e+02 angle pdb="HD21 LEU B 362 " pdb=" CD2 LEU B 362 " pdb="HD23 LEU B 362 " ideal model delta sigma weight residual 110.00 79.85 30.15 3.00e+00 1.11e-01 1.01e+02 angle pdb="HG21 THR D 240 " pdb=" CG2 THR D 240 " pdb="HG23 THR D 240 " ideal model delta sigma weight residual 109.00 79.08 29.92 3.00e+00 1.11e-01 9.95e+01 ... (remaining 74471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 18464 16.31 - 32.62: 1112 32.62 - 48.93: 332 48.93 - 65.24: 184 65.24 - 81.55: 12 Dihedral angle restraints: 20104 sinusoidal: 9784 harmonic: 10320 Sorted by residual: dihedral pdb=" CA VAL B 560 " pdb=" C VAL B 560 " pdb=" N ILE B 561 " pdb=" CA ILE B 561 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL D 560 " pdb=" C VAL D 560 " pdb=" N ILE D 561 " pdb=" CA ILE D 561 " ideal model delta harmonic sigma weight residual 180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 560 " pdb=" C VAL A 560 " pdb=" N ILE A 561 " pdb=" CA ILE A 561 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 20101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2714 0.040 - 0.079: 688 0.079 - 0.119: 218 0.119 - 0.158: 12 0.158 - 0.198: 4 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CA ARG B 232 " pdb=" N ARG B 232 " pdb=" C ARG B 232 " pdb=" CB ARG B 232 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA ARG C 232 " pdb=" N ARG C 232 " pdb=" C ARG C 232 " pdb=" CB ARG C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ARG D 232 " pdb=" N ARG D 232 " pdb=" C ARG D 232 " pdb=" CB ARG D 232 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 3633 not shown) Planarity restraints: 6880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 195 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 196 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 195 " 0.031 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 196 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 195 " -0.031 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 196 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.027 5.00e-02 4.00e+02 ... (remaining 6877 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1589 2.16 - 2.77: 75085 2.77 - 3.38: 108259 3.38 - 3.99: 130287 3.99 - 4.60: 205785 Nonbonded interactions: 521005 Sorted by model distance: nonbonded pdb=" OD1 ASP B 333 " pdb=" HG1 THR B 335 " model vdw 1.554 1.850 nonbonded pdb=" OD1 ASP C 333 " pdb=" HG1 THR C 335 " model vdw 1.554 1.850 nonbonded pdb=" OD1 ASP D 333 " pdb=" HG1 THR D 335 " model vdw 1.554 1.850 nonbonded pdb=" OD1 ASP A 333 " pdb=" HG1 THR A 335 " model vdw 1.555 1.850 nonbonded pdb=" OE1 GLU F 93 " pdb=" H GLU F 93 " model vdw 1.620 1.850 ... (remaining 521000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.640 Extract box with map and model: 5.830 Check model and map are aligned: 0.540 Set scattering table: 0.380 Process input model: 116.780 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.220 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 0.024 22232 Z= 0.190 Angle : 0.571 6.247 30408 Z= 0.317 Chirality : 0.039 0.198 3636 Planarity : 0.004 0.048 3920 Dihedral : 11.680 81.552 7260 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3052 helix: 1.93 (0.12), residues: 1616 sheet: 0.17 (0.32), residues: 256 loop : -0.62 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 463 HIS 0.003 0.001 HIS D 401 PHE 0.014 0.001 PHE B 386 TYR 0.013 0.001 TYR D 574 ARG 0.003 0.001 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 567 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 563 time to evaluate : 3.188 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: 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: 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: 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: 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 271 ARG cc_start: 0.7682 (ptm160) cc_final: 0.7454 (ttp80) REVERT: A 303 TYR cc_start: 0.7605 (t80) cc_final: 0.7213 (t80) REVERT: A 389 ILE cc_start: 0.8750 (mt) cc_final: 0.8455 (tt) REVERT: A 424 LEU cc_start: 0.7634 (tp) cc_final: 0.7397 (tt) REVERT: A 457 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7292 (mp0) REVERT: A 582 LEU cc_start: 0.7629 (tp) cc_final: 0.7413 (mt) REVERT: A 588 ASN cc_start: 0.8010 (t0) cc_final: 0.7238 (t0) REVERT: A 590 LEU cc_start: 0.8055 (mt) cc_final: 0.7736 (tp) REVERT: A 728 GLU cc_start: 0.6762 (mp0) cc_final: 0.6452 (mp0) REVERT: E 157 MET cc_start: 0.5744 (mmm) cc_final: 0.5225 (mmm) REVERT: E 173 MET cc_start: 0.7588 (ttm) cc_final: 0.7266 (ptt) REVERT: H 92 LEU cc_start: 0.5045 (tt) cc_final: 0.4820 (mm) REVERT: H 118 LYS cc_start: 0.2648 (mtmt) cc_final: 0.1159 (mttt) REVERT: B 341 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8011 (t80) REVERT: B 356 LEU cc_start: 0.7283 (tt) cc_final: 0.6983 (mt) REVERT: B 368 ASN cc_start: 0.7921 (m-40) cc_final: 0.7675 (m110) REVERT: B 389 ILE cc_start: 0.8657 (mt) cc_final: 0.8399 (tt) REVERT: B 424 LEU cc_start: 0.7609 (tp) cc_final: 0.7352 (tt) REVERT: B 457 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7231 (mp0) REVERT: B 588 ASN cc_start: 0.8182 (t0) cc_final: 0.7433 (t0) REVERT: B 590 LEU cc_start: 0.8215 (mt) cc_final: 0.7902 (tp) REVERT: B 713 MET cc_start: 0.7644 (ttp) cc_final: 0.7240 (tpp) REVERT: B 728 GLU cc_start: 0.6841 (mp0) cc_final: 0.6559 (mp0) REVERT: C 303 TYR cc_start: 0.7340 (t80) cc_final: 0.6963 (t80) REVERT: C 368 ASN cc_start: 0.7858 (m-40) cc_final: 0.7621 (m110) REVERT: C 588 ASN cc_start: 0.8046 (t0) cc_final: 0.7339 (t0) REVERT: C 590 LEU cc_start: 0.8042 (mt) cc_final: 0.7730 (tp) REVERT: D 424 LEU cc_start: 0.7962 (tp) cc_final: 0.7684 (tt) REVERT: D 457 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7121 (mp0) REVERT: D 479 LEU cc_start: 0.7724 (mt) cc_final: 0.7116 (tp) REVERT: D 707 PHE cc_start: 0.8168 (m-10) cc_final: 0.7855 (m-80) REVERT: D 710 LEU cc_start: 0.8901 (tt) cc_final: 0.8495 (mt) REVERT: D 713 MET cc_start: 0.7192 (ttp) cc_final: 0.6692 (tpp) outliers start: 4 outliers final: 3 residues processed: 567 average time/residue: 0.8076 time to fit residues: 682.7643 Evaluate side-chains 427 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 423 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain D residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 0.0770 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 chunk 241 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 overall best weight: 2.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 ASN F 94 ASN H 94 ASN D 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22232 Z= 0.313 Angle : 0.618 7.225 30408 Z= 0.331 Chirality : 0.041 0.130 3636 Planarity : 0.005 0.059 3920 Dihedral : 5.393 80.257 3340 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 13.85 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3052 helix: 1.38 (0.12), residues: 1664 sheet: 0.19 (0.32), residues: 280 loop : -0.59 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 785 HIS 0.007 0.001 HIS B 243 PHE 0.017 0.002 PHE D 226 TYR 0.015 0.001 TYR A 346 ARG 0.005 0.001 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 441 time to evaluate : 3.379 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: 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: 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: 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 229 SER cc_start: 0.8040 (p) cc_final: 0.7805 (m) REVERT: A 303 TYR cc_start: 0.8096 (t80) cc_final: 0.7845 (t80) REVERT: A 368 ASN cc_start: 0.7855 (m-40) cc_final: 0.7621 (m-40) REVERT: A 457 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7196 (mp0) REVERT: A 588 ASN cc_start: 0.8219 (t0) cc_final: 0.7472 (t0) REVERT: A 590 LEU cc_start: 0.8075 (mt) cc_final: 0.7756 (tp) REVERT: A 713 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6301 (tmm) REVERT: E 51 LYS cc_start: 0.7162 (ttmm) cc_final: 0.6017 (pttt) REVERT: E 157 MET cc_start: 0.5800 (mmm) cc_final: 0.5480 (mmm) REVERT: F 118 LYS cc_start: 0.2468 (mtmt) cc_final: 0.1199 (mttt) REVERT: G 6 LYS cc_start: 0.7549 (mmmt) cc_final: 0.7326 (mmmm) REVERT: G 92 LEU cc_start: 0.5099 (mm) cc_final: 0.4645 (mm) REVERT: H 92 LEU cc_start: 0.5070 (tt) cc_final: 0.4816 (mm) REVERT: H 118 LYS cc_start: 0.2726 (mtmt) cc_final: 0.1887 (mttp) REVERT: B 356 LEU cc_start: 0.7864 (tt) cc_final: 0.7446 (mt) REVERT: B 368 ASN cc_start: 0.7918 (m-40) cc_final: 0.7541 (m-40) REVERT: B 389 ILE cc_start: 0.8725 (mt) cc_final: 0.8366 (tt) REVERT: B 457 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7147 (mp0) REVERT: B 588 ASN cc_start: 0.8166 (t0) cc_final: 0.7521 (t0) REVERT: B 590 LEU cc_start: 0.8248 (mt) cc_final: 0.7950 (tp) REVERT: B 713 MET cc_start: 0.7906 (ttp) cc_final: 0.7702 (tmm) REVERT: C 303 TYR cc_start: 0.7865 (t80) cc_final: 0.7611 (t80) REVERT: C 368 ASN cc_start: 0.8034 (m-40) cc_final: 0.7798 (m-40) REVERT: C 588 ASN cc_start: 0.8063 (t0) cc_final: 0.7368 (t0) REVERT: C 590 LEU cc_start: 0.8113 (mt) cc_final: 0.7816 (tp) REVERT: C 713 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7095 (tpp) REVERT: D 424 LEU cc_start: 0.8133 (tp) cc_final: 0.7871 (tt) REVERT: D 457 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7202 (mp0) REVERT: D 479 LEU cc_start: 0.7736 (mt) cc_final: 0.7241 (tp) REVERT: D 713 MET cc_start: 0.7038 (ttp) cc_final: 0.6772 (tmm) outliers start: 32 outliers final: 16 residues processed: 451 average time/residue: 0.7726 time to fit residues: 529.5438 Evaluate side-chains 425 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 407 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain F residue 42 TYR Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 232 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 95 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22232 Z= 0.252 Angle : 0.559 5.986 30408 Z= 0.292 Chirality : 0.039 0.141 3636 Planarity : 0.004 0.052 3920 Dihedral : 5.241 76.920 3340 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.78 % Allowed : 15.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3052 helix: 1.63 (0.12), residues: 1676 sheet: -0.30 (0.31), residues: 304 loop : -0.53 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 463 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.001 PHE C 284 TYR 0.013 0.001 TYR A 346 ARG 0.005 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 418 time to evaluate : 3.251 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: 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: 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: 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 368 ASN cc_start: 0.7790 (m-40) cc_final: 0.7336 (m-40) REVERT: A 457 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7406 (mp0) REVERT: A 588 ASN cc_start: 0.8110 (t0) cc_final: 0.7392 (t0) REVERT: A 590 LEU cc_start: 0.8133 (mt) cc_final: 0.7815 (tp) REVERT: A 713 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6296 (tmm) REVERT: A 781 ASP cc_start: 0.7894 (t0) cc_final: 0.7606 (p0) REVERT: E 6 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7240 (mmmm) REVERT: E 51 LYS cc_start: 0.7181 (ttmm) cc_final: 0.5984 (pttt) REVERT: F 82 MET cc_start: 0.4342 (ttp) cc_final: 0.3677 (tpt) REVERT: H 92 LEU cc_start: 0.5263 (tt) cc_final: 0.4992 (mm) REVERT: H 118 LYS cc_start: 0.2366 (mtmt) cc_final: 0.1523 (mttt) REVERT: B 271 ARG cc_start: 0.8311 (ptm160) cc_final: 0.8110 (ttp80) REVERT: B 356 LEU cc_start: 0.7929 (tt) cc_final: 0.7517 (mt) REVERT: B 368 ASN cc_start: 0.7909 (m-40) cc_final: 0.7547 (m-40) REVERT: B 457 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7232 (mp0) REVERT: B 566 LEU cc_start: 0.6212 (mm) cc_final: 0.5947 (mm) REVERT: B 588 ASN cc_start: 0.8161 (t0) cc_final: 0.7474 (t0) REVERT: B 590 LEU cc_start: 0.8253 (mt) cc_final: 0.7974 (tp) REVERT: B 713 MET cc_start: 0.7702 (ttp) cc_final: 0.7297 (tmm) REVERT: B 781 ASP cc_start: 0.7986 (t0) cc_final: 0.7627 (p0) REVERT: C 303 TYR cc_start: 0.8009 (t80) cc_final: 0.7796 (t80) REVERT: C 368 ASN cc_start: 0.7992 (m-40) cc_final: 0.7623 (m-40) REVERT: C 588 ASN cc_start: 0.8088 (t0) cc_final: 0.7397 (t0) REVERT: C 590 LEU cc_start: 0.8146 (mt) cc_final: 0.7860 (tp) REVERT: C 713 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6895 (tpp) REVERT: C 728 GLU cc_start: 0.6340 (mp0) cc_final: 0.6099 (mp0) REVERT: D 457 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7298 (mp0) REVERT: D 479 LEU cc_start: 0.7725 (mt) cc_final: 0.7240 (tp) REVERT: D 588 ASN cc_start: 0.8447 (t0) cc_final: 0.7937 (t0) REVERT: D 685 MET cc_start: 0.8345 (mpp) cc_final: 0.8091 (mmm) REVERT: D 713 MET cc_start: 0.7083 (ttp) cc_final: 0.6798 (tmm) outliers start: 33 outliers final: 19 residues processed: 438 average time/residue: 0.7208 time to fit residues: 480.8529 Evaluate side-chains 425 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 404 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 297 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 528 ASN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS D 368 ASN D 528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 22232 Z= 0.392 Angle : 0.626 7.968 30408 Z= 0.329 Chirality : 0.040 0.152 3636 Planarity : 0.005 0.052 3920 Dihedral : 5.437 79.589 3340 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 16.38 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3052 helix: 1.41 (0.12), residues: 1676 sheet: -0.49 (0.31), residues: 304 loop : -0.62 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 785 HIS 0.007 0.002 HIS A 243 PHE 0.020 0.002 PHE C 284 TYR 0.019 0.001 TYR D 346 ARG 0.004 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 418 time to evaluate : 3.346 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7805 (m-40) cc_final: 0.7471 (m-40) REVERT: A 450 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7350 (mm) REVERT: A 457 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7435 (mp0) REVERT: A 588 ASN cc_start: 0.8099 (t0) cc_final: 0.7413 (t0) REVERT: A 590 LEU cc_start: 0.8137 (mt) cc_final: 0.7826 (tp) REVERT: A 713 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6290 (tmm) REVERT: E 6 LYS cc_start: 0.7716 (mmmt) cc_final: 0.7474 (mmmt) REVERT: E 51 LYS cc_start: 0.7039 (ttmm) cc_final: 0.5972 (pttt) REVERT: F 51 LYS cc_start: 0.7070 (ttmm) cc_final: 0.6711 (ttpp) REVERT: F 82 MET cc_start: 0.4154 (ttp) cc_final: 0.3518 (ttp) REVERT: H 118 LYS cc_start: 0.2864 (mtmt) cc_final: 0.1925 (mttt) REVERT: B 368 ASN cc_start: 0.8069 (m-40) cc_final: 0.7755 (m-40) REVERT: B 457 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7406 (mp0) REVERT: B 566 LEU cc_start: 0.6285 (mm) cc_final: 0.6073 (mm) REVERT: B 588 ASN cc_start: 0.8278 (t0) cc_final: 0.7625 (t0) REVERT: B 590 LEU cc_start: 0.8239 (mt) cc_final: 0.7960 (tp) REVERT: B 713 MET cc_start: 0.7673 (ttp) cc_final: 0.7256 (tmm) REVERT: C 368 ASN cc_start: 0.7993 (m-40) cc_final: 0.7624 (m-40) REVERT: C 588 ASN cc_start: 0.8202 (t0) cc_final: 0.7559 (t0) REVERT: C 590 LEU cc_start: 0.8127 (mt) cc_final: 0.7846 (tp) REVERT: C 713 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: C 728 GLU cc_start: 0.6517 (mp0) cc_final: 0.6286 (mp0) REVERT: C 781 ASP cc_start: 0.7933 (t0) cc_final: 0.7692 (p0) REVERT: D 450 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (mm) REVERT: D 457 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7320 (mp0) REVERT: D 479 LEU cc_start: 0.7743 (mt) cc_final: 0.7186 (tp) REVERT: D 588 ASN cc_start: 0.8485 (t0) cc_final: 0.8048 (t0) REVERT: D 685 MET cc_start: 0.8302 (mpp) cc_final: 0.8031 (mmm) REVERT: D 713 MET cc_start: 0.7248 (ttp) cc_final: 0.6925 (tmm) outliers start: 46 outliers final: 37 residues processed: 448 average time/residue: 0.7060 time to fit residues: 481.7409 Evaluate side-chains 444 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 403 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 205 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22232 Z= 0.262 Angle : 0.563 6.950 30408 Z= 0.291 Chirality : 0.039 0.161 3636 Planarity : 0.004 0.058 3920 Dihedral : 5.254 77.264 3340 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.32 % Allowed : 16.65 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3052 helix: 1.67 (0.13), residues: 1672 sheet: -0.60 (0.31), residues: 300 loop : -0.63 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 463 HIS 0.009 0.001 HIS A 252 PHE 0.016 0.002 PHE B 357 TYR 0.013 0.001 TYR A 253 ARG 0.007 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 415 time to evaluate : 3.274 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8385 (mt) cc_final: 0.8146 (mp) REVERT: A 368 ASN cc_start: 0.7803 (m-40) cc_final: 0.7582 (m-40) REVERT: A 457 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7438 (mp0) REVERT: A 588 ASN cc_start: 0.8143 (t0) cc_final: 0.7468 (t0) REVERT: A 590 LEU cc_start: 0.8121 (mt) cc_final: 0.7815 (tp) REVERT: A 713 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6390 (tmm) REVERT: E 6 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7537 (mmmt) REVERT: E 23 ILE cc_start: 0.7076 (mt) cc_final: 0.6850 (mt) REVERT: E 51 LYS cc_start: 0.7009 (ttmm) cc_final: 0.5905 (pttt) REVERT: F 82 MET cc_start: 0.4395 (ttp) cc_final: 0.3875 (ttp) REVERT: G 6 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7664 (mmmm) REVERT: H 45 ASP cc_start: 0.4835 (m-30) cc_final: 0.3402 (t0) REVERT: H 118 LYS cc_start: 0.2780 (mtmt) cc_final: 0.1793 (mtmt) REVERT: B 368 ASN cc_start: 0.8013 (m-40) cc_final: 0.7657 (m-40) REVERT: B 457 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7443 (mp0) REVERT: B 588 ASN cc_start: 0.8214 (t0) cc_final: 0.7580 (t0) REVERT: B 590 LEU cc_start: 0.8320 (mt) cc_final: 0.8039 (tp) REVERT: B 713 MET cc_start: 0.7674 (ttp) cc_final: 0.7248 (tmm) REVERT: C 368 ASN cc_start: 0.7946 (m-40) cc_final: 0.7609 (m-40) REVERT: C 588 ASN cc_start: 0.8202 (t0) cc_final: 0.7578 (t0) REVERT: C 590 LEU cc_start: 0.8209 (mt) cc_final: 0.7930 (tp) REVERT: C 713 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6885 (tpp) REVERT: C 728 GLU cc_start: 0.6703 (mp0) cc_final: 0.6494 (mp0) REVERT: D 457 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7311 (mp0) REVERT: D 479 LEU cc_start: 0.7807 (mt) cc_final: 0.7254 (tp) REVERT: D 588 ASN cc_start: 0.8546 (t0) cc_final: 0.8094 (t0) REVERT: D 685 MET cc_start: 0.8308 (mpp) cc_final: 0.8051 (mmm) REVERT: D 713 MET cc_start: 0.7333 (ttp) cc_final: 0.7068 (tmm) outliers start: 43 outliers final: 36 residues processed: 442 average time/residue: 0.7074 time to fit residues: 480.9188 Evaluate side-chains 442 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 404 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 40.0000 chunk 298 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22232 Z= 0.270 Angle : 0.559 6.318 30408 Z= 0.289 Chirality : 0.038 0.157 3636 Planarity : 0.004 0.050 3920 Dihedral : 5.173 68.241 3340 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.02 % Allowed : 17.35 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3052 helix: 1.77 (0.13), residues: 1656 sheet: -0.75 (0.31), residues: 300 loop : -0.72 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 463 HIS 0.005 0.001 HIS A 243 PHE 0.015 0.001 PHE C 341 TYR 0.012 0.001 TYR A 346 ARG 0.006 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 415 time to evaluate : 3.164 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7798 (m-40) cc_final: 0.7567 (m-40) REVERT: A 457 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7414 (mp0) REVERT: A 588 ASN cc_start: 0.8084 (t0) cc_final: 0.7419 (t0) REVERT: A 590 LEU cc_start: 0.8142 (mt) cc_final: 0.7841 (tp) REVERT: A 713 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6262 (tmm) REVERT: E 6 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7487 (mmmm) REVERT: E 45 ASP cc_start: 0.4433 (OUTLIER) cc_final: 0.3528 (t0) REVERT: E 51 LYS cc_start: 0.7028 (ttmm) cc_final: 0.5969 (pttt) REVERT: F 82 MET cc_start: 0.4420 (ttp) cc_final: 0.3938 (ttp) REVERT: G 45 ASP cc_start: 0.4208 (OUTLIER) cc_final: 0.3832 (t0) REVERT: H 45 ASP cc_start: 0.4970 (OUTLIER) cc_final: 0.3533 (t0) REVERT: B 368 ASN cc_start: 0.7991 (m-40) cc_final: 0.7677 (m-40) REVERT: B 457 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7503 (mp0) REVERT: B 588 ASN cc_start: 0.8188 (t0) cc_final: 0.7556 (t0) REVERT: B 590 LEU cc_start: 0.8307 (mt) cc_final: 0.8036 (tp) REVERT: B 713 MET cc_start: 0.7579 (ttp) cc_final: 0.7141 (tmm) REVERT: C 368 ASN cc_start: 0.7956 (m-40) cc_final: 0.7614 (m-40) REVERT: C 588 ASN cc_start: 0.8223 (t0) cc_final: 0.7496 (t0) REVERT: C 590 LEU cc_start: 0.8223 (mt) cc_final: 0.7947 (tp) REVERT: C 713 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6750 (tpp) REVERT: C 728 GLU cc_start: 0.6701 (mp0) cc_final: 0.6495 (mp0) REVERT: D 229 SER cc_start: 0.7992 (p) cc_final: 0.7770 (m) REVERT: D 450 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7423 (mm) REVERT: D 457 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7296 (mp0) REVERT: D 479 LEU cc_start: 0.7806 (mt) cc_final: 0.7253 (tp) REVERT: D 588 ASN cc_start: 0.8557 (t0) cc_final: 0.8094 (t0) REVERT: D 685 MET cc_start: 0.8340 (mpp) cc_final: 0.8104 (mmm) REVERT: D 713 MET cc_start: 0.7552 (ttp) cc_final: 0.7285 (tmm) outliers start: 56 outliers final: 46 residues processed: 449 average time/residue: 0.7253 time to fit residues: 503.4495 Evaluate side-chains 454 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 402 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 217 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 ASN F 41 ASN G 41 ASN B 176 HIS C 176 HIS ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 22232 Z= 0.512 Angle : 0.694 10.865 30408 Z= 0.366 Chirality : 0.043 0.187 3636 Planarity : 0.005 0.061 3920 Dihedral : 5.639 70.155 3340 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.61 % Allowed : 19.02 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3052 helix: 1.06 (0.13), residues: 1660 sheet: -1.12 (0.30), residues: 304 loop : -1.10 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 785 HIS 0.012 0.002 HIS A 252 PHE 0.030 0.002 PHE A 284 TYR 0.022 0.002 TYR C 553 ARG 0.005 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 398 time to evaluate : 3.267 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.8008 (m-40) cc_final: 0.7798 (m-40) REVERT: A 450 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 457 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7642 (mp0) REVERT: A 588 ASN cc_start: 0.8073 (t0) cc_final: 0.7422 (t0) REVERT: A 590 LEU cc_start: 0.8196 (mt) cc_final: 0.7891 (tp) REVERT: A 713 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6220 (tmm) REVERT: E 45 ASP cc_start: 0.4596 (OUTLIER) cc_final: 0.3624 (t0) REVERT: E 51 LYS cc_start: 0.6993 (ttmm) cc_final: 0.5966 (pttt) REVERT: F 45 ASP cc_start: 0.4668 (OUTLIER) cc_final: 0.3523 (t0) REVERT: G 45 ASP cc_start: 0.4310 (OUTLIER) cc_final: 0.3781 (t0) REVERT: B 158 VAL cc_start: 0.8711 (t) cc_final: 0.8338 (p) REVERT: B 368 ASN cc_start: 0.8091 (m-40) cc_final: 0.7789 (m-40) REVERT: B 457 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7562 (mp0) REVERT: B 566 LEU cc_start: 0.5573 (mm) cc_final: 0.5347 (mm) REVERT: B 588 ASN cc_start: 0.8295 (t0) cc_final: 0.7634 (t0) REVERT: B 590 LEU cc_start: 0.8348 (mt) cc_final: 0.8080 (tp) REVERT: B 713 MET cc_start: 0.7760 (ttp) cc_final: 0.7320 (tmm) REVERT: C 368 ASN cc_start: 0.8049 (m-40) cc_final: 0.7741 (m-40) REVERT: C 588 ASN cc_start: 0.8244 (t0) cc_final: 0.7508 (t0) REVERT: C 590 LEU cc_start: 0.8237 (mt) cc_final: 0.7958 (tp) REVERT: D 229 SER cc_start: 0.8091 (p) cc_final: 0.7875 (m) REVERT: D 450 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (mm) REVERT: D 457 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7372 (mp0) REVERT: D 479 LEU cc_start: 0.7767 (mt) cc_final: 0.7108 (tp) REVERT: D 588 ASN cc_start: 0.8526 (t0) cc_final: 0.8089 (t0) REVERT: D 685 MET cc_start: 0.8368 (mpp) cc_final: 0.8132 (mmm) REVERT: D 713 MET cc_start: 0.7750 (ttp) cc_final: 0.7456 (tmm) outliers start: 67 outliers final: 57 residues processed: 443 average time/residue: 0.7105 time to fit residues: 487.5459 Evaluate side-chains 453 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 390 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 177 optimal weight: 50.0000 chunk 89 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 ASN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22232 Z= 0.261 Angle : 0.563 7.045 30408 Z= 0.292 Chirality : 0.038 0.132 3636 Planarity : 0.004 0.055 3920 Dihedral : 5.333 72.463 3340 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.39 % Allowed : 19.77 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3052 helix: 1.60 (0.13), residues: 1660 sheet: -1.09 (0.30), residues: 300 loop : -0.92 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 463 HIS 0.008 0.001 HIS A 252 PHE 0.016 0.001 PHE E 106 TYR 0.017 0.001 TYR B 553 ARG 0.010 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 392 time to evaluate : 3.340 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: 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: 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: 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 368 ASN cc_start: 0.7994 (m-40) cc_final: 0.7781 (m-40) REVERT: A 450 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7515 (mm) REVERT: A 457 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7577 (mp0) REVERT: A 588 ASN cc_start: 0.8016 (t0) cc_final: 0.7337 (t0) REVERT: A 590 LEU cc_start: 0.8223 (mt) cc_final: 0.7935 (tp) REVERT: A 713 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6237 (tmm) REVERT: E 6 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7442 (mmmm) REVERT: E 45 ASP cc_start: 0.4484 (OUTLIER) cc_final: 0.3602 (t0) REVERT: E 51 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6019 (pttt) REVERT: F 45 ASP cc_start: 0.4581 (OUTLIER) cc_final: 0.3525 (t0) REVERT: G 6 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7749 (mmmm) REVERT: B 368 ASN cc_start: 0.8108 (m-40) cc_final: 0.7811 (m-40) REVERT: B 457 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7562 (mp0) REVERT: B 566 LEU cc_start: 0.5719 (mm) cc_final: 0.5485 (mm) REVERT: B 588 ASN cc_start: 0.8139 (t0) cc_final: 0.7474 (t0) REVERT: B 590 LEU cc_start: 0.8336 (mt) cc_final: 0.8074 (tp) REVERT: B 713 MET cc_start: 0.7712 (ttp) cc_final: 0.7257 (tmm) REVERT: C 368 ASN cc_start: 0.8124 (m-40) cc_final: 0.7830 (m-40) REVERT: C 566 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5831 (mm) REVERT: C 588 ASN cc_start: 0.7999 (t0) cc_final: 0.7223 (t0) REVERT: C 590 LEU cc_start: 0.8297 (mt) cc_final: 0.8028 (tp) REVERT: D 450 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7527 (mm) REVERT: D 457 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7335 (mp0) REVERT: D 479 LEU cc_start: 0.7802 (mt) cc_final: 0.7207 (tp) REVERT: D 588 ASN cc_start: 0.8510 (t0) cc_final: 0.8065 (t0) REVERT: D 713 MET cc_start: 0.7649 (ttp) cc_final: 0.7357 (tmm) outliers start: 63 outliers final: 52 residues processed: 437 average time/residue: 0.7035 time to fit residues: 475.8765 Evaluate side-chains 442 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 384 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.9990 chunk 284 optimal weight: 50.0000 chunk 259 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22232 Z= 0.171 Angle : 0.530 5.696 30408 Z= 0.272 Chirality : 0.038 0.160 3636 Planarity : 0.004 0.052 3920 Dihedral : 5.153 67.735 3340 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.75 % Allowed : 20.10 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3052 helix: 1.96 (0.13), residues: 1660 sheet: -1.04 (0.30), residues: 300 loop : -0.77 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 409 HIS 0.009 0.001 HIS A 252 PHE 0.013 0.001 PHE C 341 TYR 0.020 0.001 TYR A 553 ARG 0.009 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 392 time to evaluate : 3.428 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7952 (m-40) cc_final: 0.7717 (m-40) REVERT: A 450 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 457 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7574 (mp0) REVERT: A 588 ASN cc_start: 0.8070 (t0) cc_final: 0.7331 (t0) REVERT: A 590 LEU cc_start: 0.8224 (mt) cc_final: 0.7943 (tp) REVERT: A 713 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6285 (tmm) REVERT: E 6 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7425 (mmmm) REVERT: E 45 ASP cc_start: 0.4364 (OUTLIER) cc_final: 0.3543 (t0) REVERT: E 51 LYS cc_start: 0.7008 (ttmm) cc_final: 0.6067 (pttt) REVERT: F 45 ASP cc_start: 0.4533 (OUTLIER) cc_final: 0.3554 (t0) REVERT: G 6 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7727 (mmmm) REVERT: G 45 ASP cc_start: 0.4359 (OUTLIER) cc_final: 0.3842 (t0) REVERT: B 368 ASN cc_start: 0.8072 (m-40) cc_final: 0.7784 (m-40) REVERT: B 457 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7528 (mp0) REVERT: B 588 ASN cc_start: 0.8190 (t0) cc_final: 0.7477 (t0) REVERT: B 590 LEU cc_start: 0.8335 (mt) cc_final: 0.8078 (tp) REVERT: B 713 MET cc_start: 0.7565 (ttp) cc_final: 0.7109 (tmm) REVERT: C 368 ASN cc_start: 0.8077 (m-40) cc_final: 0.7787 (m-40) REVERT: C 566 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5778 (mm) REVERT: C 588 ASN cc_start: 0.8025 (t0) cc_final: 0.7275 (t0) REVERT: C 590 LEU cc_start: 0.8297 (mt) cc_final: 0.8031 (tp) REVERT: D 450 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (mm) REVERT: D 457 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7289 (mp0) REVERT: D 479 LEU cc_start: 0.7789 (mt) cc_final: 0.7217 (tp) REVERT: D 588 ASN cc_start: 0.8471 (t0) cc_final: 0.8041 (t0) REVERT: D 713 MET cc_start: 0.7657 (ttp) cc_final: 0.7398 (tmm) outliers start: 51 outliers final: 43 residues processed: 424 average time/residue: 0.6958 time to fit residues: 455.8712 Evaluate side-chains 438 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 388 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.9980 chunk 292 optimal weight: 40.0000 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 0.1980 chunk 203 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22232 Z= 0.219 Angle : 0.541 5.853 30408 Z= 0.279 Chirality : 0.038 0.189 3636 Planarity : 0.004 0.054 3920 Dihedral : 5.103 64.388 3340 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.80 % Allowed : 20.42 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3052 helix: 1.98 (0.13), residues: 1660 sheet: -1.03 (0.30), residues: 300 loop : -0.76 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 409 HIS 0.008 0.001 HIS A 252 PHE 0.022 0.001 PHE B 357 TYR 0.016 0.001 TYR A 553 ARG 0.014 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue VAL 433 is missing expected H atoms. Skipping. Residue LEU 434 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue TYR 439 is missing expected H atoms. Skipping. Residue SER 441 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue ILE 443 is missing expected H atoms. Skipping. Residue MET 449 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue MET 482 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 506 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LEU 511 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue ILE 516 is missing expected H atoms. Skipping. Residue THR 517 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue THR 520 is missing expected H atoms. Skipping. Residue VAL 522 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue ILE 529 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 561 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue TYR 567 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue MET 605 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue TYR 621 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue MET 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue TYR 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LEU 636 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 671 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LYS 675 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue THR 689 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue TYR 691 is missing expected H atoms. Skipping. Residue VAL 693 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 721 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue LYS 734 is missing expected H atoms. Skipping. Residue ILE 741 is missing expected H atoms. Skipping. Residue LYS 754 is missing expected H atoms. Skipping. Residue THR 763 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue SER 767 is missing expected H atoms. Skipping. Residue SER 768 is missing expected H atoms. Skipping. Residue THR 771 is missing expected H atoms. Skipping. Residue VAL 783 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 387 time to evaluate : 3.424 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 368 ASN cc_start: 0.7955 (m-40) cc_final: 0.7722 (m-40) REVERT: A 450 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 457 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7584 (mp0) REVERT: A 588 ASN cc_start: 0.8119 (t0) cc_final: 0.7335 (t0) REVERT: A 590 LEU cc_start: 0.8235 (mt) cc_final: 0.7957 (tp) REVERT: A 713 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6138 (tmm) REVERT: E 6 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7479 (mmmm) REVERT: E 45 ASP cc_start: 0.4405 (OUTLIER) cc_final: 0.3571 (t0) REVERT: E 51 LYS cc_start: 0.7024 (ttmm) cc_final: 0.6066 (pttt) REVERT: F 45 ASP cc_start: 0.4537 (OUTLIER) cc_final: 0.3570 (t0) REVERT: G 45 ASP cc_start: 0.4377 (OUTLIER) cc_final: 0.3852 (t0) REVERT: H 45 ASP cc_start: 0.4581 (m-30) cc_final: 0.3190 (t0) REVERT: B 368 ASN cc_start: 0.8094 (m-40) cc_final: 0.7811 (m-40) REVERT: B 457 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 588 ASN cc_start: 0.8146 (t0) cc_final: 0.7434 (t0) REVERT: B 590 LEU cc_start: 0.8345 (mt) cc_final: 0.8092 (tp) REVERT: B 713 MET cc_start: 0.7508 (ttp) cc_final: 0.7037 (tmm) REVERT: C 368 ASN cc_start: 0.8034 (m-40) cc_final: 0.7717 (m-40) REVERT: C 566 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5672 (mm) REVERT: C 588 ASN cc_start: 0.8041 (t0) cc_final: 0.7284 (t0) REVERT: C 590 LEU cc_start: 0.8310 (mt) cc_final: 0.8047 (tp) REVERT: D 450 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7569 (mm) REVERT: D 457 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7321 (mp0) REVERT: D 479 LEU cc_start: 0.7831 (mt) cc_final: 0.7276 (tp) REVERT: D 588 ASN cc_start: 0.8488 (t0) cc_final: 0.8053 (t0) REVERT: D 713 MET cc_start: 0.7719 (ttp) cc_final: 0.7443 (tmm) outliers start: 52 outliers final: 45 residues processed: 422 average time/residue: 0.6986 time to fit residues: 455.3258 Evaluate side-chains 437 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 385 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain E residue 42 TYR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 702 TYR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.235159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184998 restraints weight = 100545.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162771 restraints weight = 108519.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161555 restraints weight = 88075.451| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22232 Z= 0.284 Angle : 0.566 6.793 30408 Z= 0.293 Chirality : 0.039 0.159 3636 Planarity : 0.004 0.070 3920 Dihedral : 5.145 62.322 3340 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 20.10 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3052 helix: 1.86 (0.13), residues: 1660 sheet: -1.12 (0.31), residues: 296 loop : -0.84 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 409 HIS 0.007 0.001 HIS A 252 PHE 0.026 0.002 PHE B 357 TYR 0.014 0.001 TYR A 553 ARG 0.013 0.001 ARG C 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8957.07 seconds wall clock time: 159 minutes 15.76 seconds (9555.76 seconds total)