Starting phenix.real_space_refine on Mon Mar 25 15:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4m_27892/03_2024/8e4m_27892_trim_updated.pdb" } resolution = 3.44 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= 0.005 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 16 5.49 5 S 96 5.16 5 C 17036 2.51 5 N 4307 2.21 5 O 4636 1.98 5 H 23500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49595 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "B" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "C" Number of atoms: 12333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12333 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 776 Unresolved non-hydrogen angles: 980 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "D" Number of atoms: 12334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 12334 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 20, 'TRANS': 860} Chain breaks: 14 Unresolved non-hydrogen bonds: 775 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 20, 'TRP:plan': 3, 'ASP:plan': 19, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 477 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' CA': 1, 'PIO': 1, 'ULO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 22.82, per 1000 atoms: 0.46 Number of scatterers: 49595 At special positions: 0 Unit cell: (148.73, 148.73, 147.66, 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) Ca 4 19.99 S 96 16.00 P 16 15.00 O 4636 8.00 N 4307 7.00 C 17036 6.00 H 23500 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: 39.97 Conformation dependent library (CDL) restraints added in 6.2 seconds 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 8 sheets defined 68.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.66 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'A' and resid 608 through 635 Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 734 through 757 Processing helix chain 'A' and resid 766 through 786 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 953 through 987 Proline residue: A 958 - end of helix removed outlier: 3.893A pdb=" N PHE A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A1018 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA A1054 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A1070 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1103 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 608 through 635 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 734 through 757 Processing helix chain 'B' and resid 766 through 786 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU B 906 " --> pdb=" O SER B 902 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 953 through 987 Proline residue: B 958 - end of helix removed outlier: 3.893A pdb=" N PHE B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B1018 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA B1054 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B1070 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1103 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE C 165 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 Processing helix chain 'C' and resid 608 through 635 Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 666 through 669 No H-bonds generated for 'chain 'C' and resid 666 through 669' Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 703 through 706' Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 734 through 757 Processing helix chain 'C' and resid 766 through 786 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 807 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE C 858 " --> pdb=" O GLY C 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 869 " --> pdb=" O ILE C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 917 through 921 Processing helix chain 'C' and resid 953 through 987 Proline residue: C 958 - end of helix removed outlier: 3.893A pdb=" N PHE C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1024 removed outlier: 5.443A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C1018 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA C1054 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C1070 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1103 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.722A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.607A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.776A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 4.593A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 521 through 533 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.758A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 Processing helix chain 'D' and resid 608 through 635 Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 703 through 706 removed outlier: 3.679A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 703 through 706' Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 734 through 757 Processing helix chain 'D' and resid 766 through 786 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 797 through 816 removed outlier: 3.558A pdb=" N LEU D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 807 " --> pdb=" O THR D 803 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 808 " --> pdb=" O LEU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 849 removed outlier: 4.007A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 889 removed outlier: 3.635A pdb=" N ILE D 858 " --> pdb=" O GLY D 854 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE D 869 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 912 removed outlier: 3.726A pdb=" N GLU D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 917 through 921 Processing helix chain 'D' and resid 953 through 987 Proline residue: D 958 - end of helix removed outlier: 3.893A pdb=" N PHE D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1007 removed outlier: 3.772A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1024 removed outlier: 5.444A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE D1018 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1073 removed outlier: 3.890A pdb=" N ALA D1054 " --> pdb=" O GLU D1051 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D1070 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 119 Processing sheet with id= B, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS A 326 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 305 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 328 " --> pdb=" O ALA A 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 116 through 119 Processing sheet with id= D, first strand: chain 'B' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS B 326 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA B 305 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 328 " --> pdb=" O ALA B 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 116 through 119 Processing sheet with id= F, first strand: chain 'C' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS C 326 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA C 305 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 328 " --> pdb=" O ALA C 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 116 through 119 Processing sheet with id= H, first strand: chain 'D' and resid 302 through 305 removed outlier: 6.464A pdb=" N CYS D 326 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 305 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 328 " --> pdb=" O ALA D 305 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1636 hydrogen bonds defined for protein. 4560 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: 19.02 Time building geometry restraints manager: 41.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 23456 1.03 - 1.24: 1615 1.24 - 1.44: 10005 1.44 - 1.65: 14899 1.65 - 1.86: 168 Bond restraints: 50143 Sorted by residual: bond pdb=" C5A PIO D1201 " pdb=" C6A PIO D1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO C1201 " pdb=" C6A PIO C1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO A1201 " pdb=" C6A PIO A1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5A PIO B1201 " pdb=" C6A PIO B1201 " ideal model delta sigma weight residual 1.527 1.579 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C1B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sigma weight residual 1.399 1.448 -0.049 2.00e-02 2.50e+03 5.91e+00 ... (remaining 50138 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 642 106.97 - 113.74: 56505 113.74 - 120.50: 17961 120.50 - 127.26: 14381 127.26 - 134.03: 292 Bond angle restraints: 89781 Sorted by residual: angle pdb=" C ILE B 701 " pdb=" N ILE B 702 " pdb=" CA ILE B 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE C 701 " pdb=" N ILE C 702 " pdb=" CA ILE C 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE A 701 " pdb=" N ILE A 702 " pdb=" CA ILE A 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" C ILE D 701 " pdb=" N ILE D 702 " pdb=" CA ILE D 702 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" N ILE D 403 " pdb=" CA ILE D 403 " pdb=" C ILE D 403 " ideal model delta sigma weight residual 111.90 109.30 2.60 8.10e-01 1.52e+00 1.03e+01 ... (remaining 89776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.83: 21927 12.83 - 25.66: 1431 25.66 - 38.49: 372 38.49 - 51.32: 236 51.32 - 64.15: 140 Dihedral angle restraints: 24106 sinusoidal: 11644 harmonic: 12462 Sorted by residual: dihedral pdb=" CA GLY C 708 " pdb=" C GLY C 708 " pdb=" N LEU C 709 " pdb=" CA LEU C 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY A 708 " pdb=" C GLY A 708 " pdb=" N LEU A 709 " pdb=" CA LEU A 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY D 708 " pdb=" C GLY D 708 " pdb=" N LEU D 709 " pdb=" CA LEU D 709 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 24103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3400 0.035 - 0.070: 654 0.070 - 0.105: 212 0.105 - 0.141: 53 0.141 - 0.176: 4 Chirality restraints: 4323 Sorted by residual: chirality pdb=" CA THR D 982 " pdb=" N THR D 982 " pdb=" C THR D 982 " pdb=" CB THR D 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA THR C 982 " pdb=" N THR C 982 " pdb=" C THR C 982 " pdb=" CB THR C 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA THR B 982 " pdb=" N THR B 982 " pdb=" C THR B 982 " pdb=" CB THR B 982 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 4320 not shown) Planarity restraints: 7884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 982 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C THR B 982 " -0.047 2.00e-02 2.50e+03 pdb=" O THR B 982 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL B 983 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 982 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C THR A 982 " -0.047 2.00e-02 2.50e+03 pdb=" O THR A 982 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 983 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 982 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C THR C 982 " 0.047 2.00e-02 2.50e+03 pdb=" O THR C 982 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL C 983 " -0.016 2.00e-02 2.50e+03 ... (remaining 7881 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2521 2.20 - 2.80: 98557 2.80 - 3.40: 131547 3.40 - 4.00: 162144 4.00 - 4.60: 255198 Nonbonded interactions: 649967 Sorted by model distance: nonbonded pdb=" O GLY C 684 " pdb="HH22 ARG C 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY D 684 " pdb="HH22 ARG D 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY A 684 " pdb="HH22 ARG A 713 " model vdw 1.603 1.850 nonbonded pdb=" O GLY B 684 " pdb="HH22 ARG B 713 " model vdw 1.603 1.850 nonbonded pdb=" HG1 THR A 494 " pdb=" O PHE A 531 " model vdw 1.615 1.850 ... (remaining 649962 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' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) selection = (chain 'B' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) selection = chain 'C' selection = (chain 'D' and ((resid 40 and (name CA or name C or name O or name CB or name HA \ )) or resid 41 through 1104 or resid 1201 through 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.790 Extract box with map and model: 6.230 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 157.330 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.230 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 0.052 26643 Z= 0.194 Angle : 0.448 5.349 36358 Z= 0.253 Chirality : 0.034 0.176 4323 Planarity : 0.003 0.058 4496 Dihedral : 10.726 64.155 8628 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % 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: 3.12 (0.15), residues: 3404 helix: 2.91 (0.11), residues: 2516 sheet: 0.74 (0.38), residues: 176 loop : -0.85 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 877 HIS 0.003 0.001 HIS C 259 PHE 0.009 0.001 PHE D 912 TYR 0.007 0.001 TYR B 826 ARG 0.002 0.000 ARG D 885 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 612 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 4.038 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: A 138 HIS cc_start: 0.6511 (m-70) cc_final: 0.6059 (m90) REVERT: A 146 ILE cc_start: 0.8285 (pt) cc_final: 0.7934 (mp) REVERT: A 170 TYR cc_start: 0.8701 (t80) cc_final: 0.8456 (t80) REVERT: A 752 PHE cc_start: 0.7250 (t80) cc_final: 0.6956 (t80) REVERT: A 1016 VAL cc_start: 0.7475 (p) cc_final: 0.7263 (p) REVERT: B 138 HIS cc_start: 0.6515 (m-70) cc_final: 0.6063 (m90) REVERT: B 146 ILE cc_start: 0.8285 (pt) cc_final: 0.7934 (mp) REVERT: B 170 TYR cc_start: 0.8703 (t80) cc_final: 0.8456 (t80) REVERT: B 752 PHE cc_start: 0.7251 (t80) cc_final: 0.6956 (t80) REVERT: B 1016 VAL cc_start: 0.7475 (p) cc_final: 0.7262 (p) REVERT: C 138 HIS cc_start: 0.6515 (m-70) cc_final: 0.6062 (m90) REVERT: C 146 ILE cc_start: 0.8287 (pt) cc_final: 0.7936 (mp) REVERT: C 170 TYR cc_start: 0.8702 (t80) cc_final: 0.8456 (t80) REVERT: C 752 PHE cc_start: 0.7248 (t80) cc_final: 0.6956 (t80) REVERT: C 1016 VAL cc_start: 0.7473 (p) cc_final: 0.7261 (p) REVERT: D 138 HIS cc_start: 0.6513 (m-70) cc_final: 0.6063 (m90) REVERT: D 146 ILE cc_start: 0.8285 (pt) cc_final: 0.7935 (mp) REVERT: D 170 TYR cc_start: 0.8702 (t80) cc_final: 0.8454 (t80) REVERT: D 752 PHE cc_start: 0.7245 (t80) cc_final: 0.6953 (t80) REVERT: D 1016 VAL cc_start: 0.7476 (p) cc_final: 0.7264 (p) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.7301 time to fit residues: 718.0159 Evaluate side-chains 401 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 3.9990 chunk 266 optimal weight: 40.0000 chunk 148 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 275 optimal weight: 0.3980 chunk 106 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN B 681 GLN C 681 GLN D 681 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 26643 Z= 0.426 Angle : 0.583 5.254 36358 Z= 0.322 Chirality : 0.038 0.151 4323 Planarity : 0.004 0.056 4496 Dihedral : 7.102 65.090 3820 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.05 % Allowed : 11.60 % Favored : 86.35 % 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: 2.33 (0.15), residues: 3404 helix: 2.36 (0.10), residues: 2476 sheet: 0.22 (0.35), residues: 176 loop : -0.98 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C1055 HIS 0.011 0.001 HIS B 765 PHE 0.013 0.002 PHE B 629 TYR 0.010 0.001 TYR D 295 ARG 0.004 0.001 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 400 time to evaluate : 4.205 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: A 138 HIS cc_start: 0.6165 (m-70) cc_final: 0.5848 (m90) REVERT: A 170 TYR cc_start: 0.8766 (t80) cc_final: 0.8456 (t80) REVERT: A 298 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8039 (mmtm) REVERT: A 863 MET cc_start: 0.7555 (mmp) cc_final: 0.6737 (mmm) REVERT: B 138 HIS cc_start: 0.6165 (m-70) cc_final: 0.5850 (m90) REVERT: B 170 TYR cc_start: 0.8765 (t80) cc_final: 0.8454 (t80) REVERT: B 298 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8039 (mmtm) REVERT: B 863 MET cc_start: 0.7558 (mmp) cc_final: 0.6739 (mmm) REVERT: C 138 HIS cc_start: 0.6164 (m-70) cc_final: 0.5848 (m90) REVERT: C 170 TYR cc_start: 0.8765 (t80) cc_final: 0.8454 (t80) REVERT: C 298 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8039 (mmtm) REVERT: C 863 MET cc_start: 0.7559 (mmp) cc_final: 0.6740 (mmm) REVERT: D 138 HIS cc_start: 0.6167 (m-70) cc_final: 0.5850 (m90) REVERT: D 170 TYR cc_start: 0.8765 (t80) cc_final: 0.8453 (t80) REVERT: D 298 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8037 (mmtm) REVERT: D 863 MET cc_start: 0.7557 (mmp) cc_final: 0.6739 (mmm) outliers start: 48 outliers final: 36 residues processed: 432 average time/residue: 0.8019 time to fit residues: 565.5809 Evaluate side-chains 372 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 336 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 865 ILE Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 30.0000 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 320 optimal weight: 2.9990 chunk 345 optimal weight: 0.4980 chunk 285 optimal weight: 20.0000 chunk 317 optimal weight: 0.0270 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN B 973 ASN C 973 ASN D 973 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26643 Z= 0.205 Angle : 0.469 5.998 36358 Z= 0.253 Chirality : 0.034 0.138 4323 Planarity : 0.004 0.056 4496 Dihedral : 6.845 70.594 3820 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.37 % Allowed : 14.68 % Favored : 83.96 % 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: 2.55 (0.15), residues: 3404 helix: 2.55 (0.11), residues: 2480 sheet: 0.31 (0.35), residues: 176 loop : -1.05 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 877 HIS 0.002 0.001 HIS B 765 PHE 0.011 0.001 PHE C 155 TYR 0.006 0.001 TYR A 981 ARG 0.002 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 360 time to evaluate : 4.441 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: A 138 HIS cc_start: 0.6268 (m-70) cc_final: 0.5898 (m90) REVERT: A 170 TYR cc_start: 0.8740 (t80) cc_final: 0.8428 (t80) REVERT: A 842 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8069 (tpp-160) REVERT: B 138 HIS cc_start: 0.6266 (m-70) cc_final: 0.5899 (m90) REVERT: B 170 TYR cc_start: 0.8742 (t80) cc_final: 0.8427 (t80) REVERT: B 842 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8070 (tpp-160) REVERT: C 138 HIS cc_start: 0.6268 (m-70) cc_final: 0.5899 (m90) REVERT: C 170 TYR cc_start: 0.8741 (t80) cc_final: 0.8428 (t80) REVERT: C 842 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8069 (tpp-160) REVERT: D 138 HIS cc_start: 0.6270 (m-70) cc_final: 0.5898 (m90) REVERT: D 170 TYR cc_start: 0.8741 (t80) cc_final: 0.8428 (t80) REVERT: D 842 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8068 (tpp-160) outliers start: 32 outliers final: 20 residues processed: 388 average time/residue: 0.7741 time to fit residues: 489.8262 Evaluate side-chains 367 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 343 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 26643 Z= 0.270 Angle : 0.487 5.126 36358 Z= 0.264 Chirality : 0.035 0.139 4323 Planarity : 0.004 0.056 4496 Dihedral : 6.844 75.883 3820 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.05 % Allowed : 15.02 % Favored : 82.94 % 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: 2.45 (0.15), residues: 3404 helix: 2.47 (0.11), residues: 2472 sheet: 0.21 (0.34), residues: 176 loop : -0.99 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1055 HIS 0.003 0.001 HIS B 765 PHE 0.015 0.001 PHE A 809 TYR 0.008 0.001 TYR D 981 ARG 0.004 0.000 ARG C 784 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 344 time to evaluate : 4.145 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: A 138 HIS cc_start: 0.6621 (m-70) cc_final: 0.6246 (m90) REVERT: A 170 TYR cc_start: 0.8725 (t80) cc_final: 0.8388 (t80) REVERT: A 458 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (tt) REVERT: A 842 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8017 (tpp-160) REVERT: A 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8336 (tp-100) REVERT: B 138 HIS cc_start: 0.6623 (m-70) cc_final: 0.6247 (m90) REVERT: B 170 TYR cc_start: 0.8725 (t80) cc_final: 0.8387 (t80) REVERT: B 458 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 842 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8019 (tpp-160) REVERT: B 1003 GLN cc_start: 0.9045 (tp40) cc_final: 0.8337 (tp-100) REVERT: C 138 HIS cc_start: 0.6622 (m-70) cc_final: 0.6246 (m90) REVERT: C 170 TYR cc_start: 0.8725 (t80) cc_final: 0.8387 (t80) REVERT: C 458 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8239 (tt) REVERT: C 842 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8016 (tpp-160) REVERT: C 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8335 (tp-100) REVERT: D 138 HIS cc_start: 0.6621 (m-70) cc_final: 0.6247 (m90) REVERT: D 170 TYR cc_start: 0.8725 (t80) cc_final: 0.8386 (t80) REVERT: D 458 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8240 (tt) REVERT: D 842 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8017 (tpp-160) REVERT: D 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8336 (tp-100) outliers start: 48 outliers final: 36 residues processed: 372 average time/residue: 0.7434 time to fit residues: 456.9232 Evaluate side-chains 380 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 336 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.9990 chunk 193 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 290 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 173 optimal weight: 30.0000 chunk 305 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 26643 Z= 0.175 Angle : 0.449 5.509 36358 Z= 0.240 Chirality : 0.034 0.139 4323 Planarity : 0.004 0.054 4496 Dihedral : 6.666 79.025 3820 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.71 % Allowed : 15.02 % Favored : 83.28 % 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: 2.70 (0.15), residues: 3404 helix: 2.69 (0.11), residues: 2456 sheet: 0.26 (0.35), residues: 176 loop : -0.95 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 994 HIS 0.002 0.001 HIS B 765 PHE 0.012 0.001 PHE B 809 TYR 0.009 0.001 TYR D 981 ARG 0.003 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 4.067 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: A 138 HIS cc_start: 0.6611 (m-70) cc_final: 0.6235 (m90) REVERT: A 170 TYR cc_start: 0.8692 (t80) cc_final: 0.8359 (t80) REVERT: A 842 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8179 (tpp-160) REVERT: A 870 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 1003 GLN cc_start: 0.9007 (tp40) cc_final: 0.8322 (tp-100) REVERT: B 138 HIS cc_start: 0.6610 (m-70) cc_final: 0.6235 (m90) REVERT: B 170 TYR cc_start: 0.8691 (t80) cc_final: 0.8359 (t80) REVERT: B 842 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8180 (tpp-160) REVERT: B 870 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7005 (t80) REVERT: B 1003 GLN cc_start: 0.9009 (tp40) cc_final: 0.8324 (tp-100) REVERT: C 138 HIS cc_start: 0.6608 (m-70) cc_final: 0.6234 (m90) REVERT: C 170 TYR cc_start: 0.8692 (t80) cc_final: 0.8357 (t80) REVERT: C 842 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8179 (tpp-160) REVERT: C 870 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7005 (t80) REVERT: C 1003 GLN cc_start: 0.9008 (tp40) cc_final: 0.8323 (tp-100) REVERT: D 138 HIS cc_start: 0.6609 (m-70) cc_final: 0.6235 (m90) REVERT: D 170 TYR cc_start: 0.8692 (t80) cc_final: 0.8357 (t80) REVERT: D 842 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8178 (tpp-160) REVERT: D 870 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7004 (t80) REVERT: D 1003 GLN cc_start: 0.9007 (tp40) cc_final: 0.8323 (tp-100) outliers start: 40 outliers final: 32 residues processed: 384 average time/residue: 0.7217 time to fit residues: 457.8451 Evaluate side-chains 392 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1050 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1050 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1050 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 26643 Z= 0.363 Angle : 0.531 5.350 36358 Z= 0.291 Chirality : 0.036 0.146 4323 Planarity : 0.004 0.055 4496 Dihedral : 6.923 86.454 3820 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.90 % Allowed : 15.02 % Favored : 82.08 % 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: 2.13 (0.15), residues: 3404 helix: 2.30 (0.10), residues: 2456 sheet: -0.09 (0.34), residues: 176 loop : -1.22 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1055 HIS 0.003 0.001 HIS A 765 PHE 0.015 0.002 PHE A 809 TYR 0.010 0.001 TYR A 506 ARG 0.003 0.000 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 353 time to evaluate : 4.326 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: A 138 HIS cc_start: 0.6731 (m-70) cc_final: 0.6373 (m90) REVERT: A 170 TYR cc_start: 0.8729 (t80) cc_final: 0.8360 (t80) REVERT: A 697 LEU cc_start: 0.8417 (mp) cc_final: 0.8119 (tt) REVERT: A 770 ILE cc_start: 0.8906 (mt) cc_final: 0.8634 (mm) REVERT: B 138 HIS cc_start: 0.6733 (m-70) cc_final: 0.6374 (m90) REVERT: B 170 TYR cc_start: 0.8727 (t80) cc_final: 0.8360 (t80) REVERT: B 697 LEU cc_start: 0.8417 (mp) cc_final: 0.8117 (tt) REVERT: B 770 ILE cc_start: 0.8908 (mt) cc_final: 0.8644 (mm) REVERT: C 138 HIS cc_start: 0.6732 (m-70) cc_final: 0.6371 (m90) REVERT: C 170 TYR cc_start: 0.8729 (t80) cc_final: 0.8360 (t80) REVERT: C 697 LEU cc_start: 0.8418 (mp) cc_final: 0.8119 (tt) REVERT: C 770 ILE cc_start: 0.8908 (mt) cc_final: 0.8644 (mm) REVERT: D 138 HIS cc_start: 0.6733 (m-70) cc_final: 0.6373 (m90) REVERT: D 170 TYR cc_start: 0.8729 (t80) cc_final: 0.8359 (t80) REVERT: D 697 LEU cc_start: 0.8418 (mp) cc_final: 0.8119 (tt) REVERT: D 770 ILE cc_start: 0.8908 (mt) cc_final: 0.8644 (mm) outliers start: 68 outliers final: 48 residues processed: 405 average time/residue: 0.7314 time to fit residues: 491.1327 Evaluate side-chains 375 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 327 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 40.0000 chunk 38 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 339 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 26643 Z= 0.274 Angle : 0.483 5.844 36358 Z= 0.262 Chirality : 0.035 0.144 4323 Planarity : 0.004 0.056 4496 Dihedral : 6.613 75.825 3820 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.56 % Allowed : 15.36 % Favored : 82.08 % 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: 2.19 (0.15), residues: 3404 helix: 2.38 (0.11), residues: 2456 sheet: -0.34 (0.34), residues: 176 loop : -1.26 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 877 HIS 0.003 0.001 HIS C 765 PHE 0.011 0.001 PHE C 809 TYR 0.009 0.001 TYR C 981 ARG 0.003 0.000 ARG D 829 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 355 time to evaluate : 3.972 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: A 138 HIS cc_start: 0.6603 (m-70) cc_final: 0.6273 (m90) REVERT: A 170 TYR cc_start: 0.8723 (t80) cc_final: 0.8369 (t80) REVERT: A 697 LEU cc_start: 0.8419 (mp) cc_final: 0.8128 (tt) REVERT: A 770 ILE cc_start: 0.8893 (mt) cc_final: 0.8617 (mm) REVERT: B 138 HIS cc_start: 0.6600 (m-70) cc_final: 0.6271 (m90) REVERT: B 170 TYR cc_start: 0.8701 (t80) cc_final: 0.8343 (t80) REVERT: B 697 LEU cc_start: 0.8419 (mp) cc_final: 0.8127 (tt) REVERT: B 770 ILE cc_start: 0.8892 (mt) cc_final: 0.8616 (mm) REVERT: C 138 HIS cc_start: 0.6601 (m-70) cc_final: 0.6271 (m90) REVERT: C 170 TYR cc_start: 0.8702 (t80) cc_final: 0.8343 (t80) REVERT: C 697 LEU cc_start: 0.8419 (mp) cc_final: 0.8127 (tt) REVERT: C 770 ILE cc_start: 0.8892 (mt) cc_final: 0.8616 (mm) REVERT: D 138 HIS cc_start: 0.6602 (m-70) cc_final: 0.6271 (m90) REVERT: D 170 TYR cc_start: 0.8702 (t80) cc_final: 0.8343 (t80) REVERT: D 697 LEU cc_start: 0.8419 (mp) cc_final: 0.8127 (tt) REVERT: D 770 ILE cc_start: 0.8892 (mt) cc_final: 0.8615 (mm) outliers start: 60 outliers final: 56 residues processed: 399 average time/residue: 0.7289 time to fit residues: 482.4036 Evaluate side-chains 404 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 348 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1050 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1050 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1050 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26643 Z= 0.220 Angle : 0.466 5.858 36358 Z= 0.251 Chirality : 0.034 0.144 4323 Planarity : 0.004 0.055 4496 Dihedral : 6.446 72.241 3820 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.56 % Allowed : 15.53 % Favored : 81.91 % 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: 2.35 (0.15), residues: 3404 helix: 2.51 (0.11), residues: 2456 sheet: -0.35 (0.34), residues: 176 loop : -1.26 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 877 HIS 0.006 0.001 HIS B 500 PHE 0.019 0.001 PHE C1013 TYR 0.007 0.001 TYR A 506 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 360 time to evaluate : 4.013 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: A 138 HIS cc_start: 0.6643 (m-70) cc_final: 0.6310 (m90) REVERT: A 170 TYR cc_start: 0.8709 (t80) cc_final: 0.8370 (t80) REVERT: A 697 LEU cc_start: 0.8428 (mp) cc_final: 0.8139 (tt) REVERT: A 770 ILE cc_start: 0.8899 (mt) cc_final: 0.8620 (mm) REVERT: A 842 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8082 (tpp-160) REVERT: A 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8448 (tp-100) REVERT: B 138 HIS cc_start: 0.6641 (m-70) cc_final: 0.6311 (m90) REVERT: B 170 TYR cc_start: 0.8710 (t80) cc_final: 0.8372 (t80) REVERT: B 697 LEU cc_start: 0.8428 (mp) cc_final: 0.8139 (tt) REVERT: B 770 ILE cc_start: 0.8899 (mt) cc_final: 0.8620 (mm) REVERT: B 842 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8085 (tpp-160) REVERT: B 1003 GLN cc_start: 0.9044 (tp40) cc_final: 0.8450 (tp-100) REVERT: C 138 HIS cc_start: 0.6640 (m-70) cc_final: 0.6309 (m90) REVERT: C 170 TYR cc_start: 0.8710 (t80) cc_final: 0.8372 (t80) REVERT: C 697 LEU cc_start: 0.8428 (mp) cc_final: 0.8137 (tt) REVERT: C 770 ILE cc_start: 0.8899 (mt) cc_final: 0.8620 (mm) REVERT: C 842 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8085 (tpp-160) REVERT: C 1003 GLN cc_start: 0.9042 (tp40) cc_final: 0.8449 (tp-100) REVERT: D 138 HIS cc_start: 0.6639 (m-70) cc_final: 0.6308 (m90) REVERT: D 170 TYR cc_start: 0.8709 (t80) cc_final: 0.8369 (t80) REVERT: D 697 LEU cc_start: 0.8426 (mp) cc_final: 0.8137 (tt) REVERT: D 770 ILE cc_start: 0.8899 (mt) cc_final: 0.8620 (mm) REVERT: D 842 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8084 (tpp-160) REVERT: D 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8447 (tp-100) outliers start: 60 outliers final: 56 residues processed: 404 average time/residue: 0.7226 time to fit residues: 484.0147 Evaluate side-chains 402 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 342 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1050 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1050 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1050 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26643 Z= 0.206 Angle : 0.459 5.907 36358 Z= 0.247 Chirality : 0.034 0.139 4323 Planarity : 0.004 0.056 4496 Dihedral : 6.277 67.516 3820 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.22 % Allowed : 15.53 % Favored : 82.25 % 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: 2.43 (0.15), residues: 3404 helix: 2.57 (0.11), residues: 2460 sheet: -0.37 (0.34), residues: 176 loop : -1.20 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 877 HIS 0.009 0.001 HIS C 500 PHE 0.019 0.001 PHE D1013 TYR 0.010 0.001 TYR A 981 ARG 0.003 0.000 ARG D 829 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 356 time to evaluate : 4.074 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: A 170 TYR cc_start: 0.8699 (t80) cc_final: 0.8361 (t80) REVERT: A 260 LEU cc_start: 0.8119 (mt) cc_final: 0.7836 (mt) REVERT: A 631 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8114 (mp0) REVERT: A 697 LEU cc_start: 0.8439 (mp) cc_final: 0.8236 (tt) REVERT: A 770 ILE cc_start: 0.8921 (mt) cc_final: 0.8639 (mm) REVERT: A 842 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8133 (tpp-160) REVERT: A 1003 GLN cc_start: 0.9041 (tp40) cc_final: 0.8458 (tp-100) REVERT: B 170 TYR cc_start: 0.8700 (t80) cc_final: 0.8364 (t80) REVERT: B 260 LEU cc_start: 0.8117 (mt) cc_final: 0.7834 (mt) REVERT: B 631 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8114 (mp0) REVERT: B 697 LEU cc_start: 0.8438 (mp) cc_final: 0.8234 (tt) REVERT: B 770 ILE cc_start: 0.8920 (mt) cc_final: 0.8639 (mm) REVERT: B 842 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8136 (tpp-160) REVERT: B 1003 GLN cc_start: 0.9043 (tp40) cc_final: 0.8460 (tp-100) REVERT: C 170 TYR cc_start: 0.8701 (t80) cc_final: 0.8364 (t80) REVERT: C 260 LEU cc_start: 0.8119 (mt) cc_final: 0.7835 (mt) REVERT: C 697 LEU cc_start: 0.8437 (mp) cc_final: 0.8233 (tt) REVERT: C 770 ILE cc_start: 0.8920 (mt) cc_final: 0.8639 (mm) REVERT: C 842 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8134 (tpp-160) REVERT: C 1003 GLN cc_start: 0.9039 (tp40) cc_final: 0.8457 (tp-100) REVERT: D 170 TYR cc_start: 0.8700 (t80) cc_final: 0.8363 (t80) REVERT: D 260 LEU cc_start: 0.8118 (mt) cc_final: 0.7835 (mt) REVERT: D 631 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8115 (mp0) REVERT: D 697 LEU cc_start: 0.8439 (mp) cc_final: 0.8235 (tt) REVERT: D 770 ILE cc_start: 0.8920 (mt) cc_final: 0.8638 (mm) REVERT: D 842 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8135 (tpp-160) REVERT: D 1003 GLN cc_start: 0.9041 (tp40) cc_final: 0.8459 (tp-100) outliers start: 52 outliers final: 48 residues processed: 388 average time/residue: 0.7292 time to fit residues: 467.3244 Evaluate side-chains 396 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 344 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1050 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1050 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1050 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26643 Z= 0.275 Angle : 0.482 5.785 36358 Z= 0.261 Chirality : 0.035 0.148 4323 Planarity : 0.004 0.055 4496 Dihedral : 6.249 64.419 3820 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.56 % Allowed : 15.02 % Favored : 82.42 % 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: 2.28 (0.15), residues: 3404 helix: 2.44 (0.10), residues: 2460 sheet: -0.42 (0.34), residues: 176 loop : -1.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 877 HIS 0.008 0.001 HIS C 500 PHE 0.012 0.001 PHE D 629 TYR 0.008 0.001 TYR B 506 ARG 0.004 0.000 ARG D 829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6808 Ramachandran restraints generated. 3404 Oldfield, 0 Emsley, 3404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue MET 161 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue TYR 793 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue TYR 908 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue THR 956 is missing expected H atoms. Skipping. Residue ILE 957 is missing expected H atoms. Skipping. Residue LEU 959 is missing expected H atoms. Skipping. Residue VAL 960 is missing expected H atoms. Skipping. Residue ILE 962 is missing expected H atoms. Skipping. Residue MET 964 is missing expected H atoms. Skipping. Residue LEU 965 is missing expected H atoms. Skipping. Residue LYS 1060 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 412 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 352 time to evaluate : 4.062 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: A 170 TYR cc_start: 0.8692 (t80) cc_final: 0.8343 (t80) REVERT: A 260 LEU cc_start: 0.8128 (mt) cc_final: 0.7852 (mt) REVERT: A 770 ILE cc_start: 0.8936 (mt) cc_final: 0.8657 (mm) REVERT: A 842 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8045 (tpp-160) REVERT: A 1003 GLN cc_start: 0.9063 (tp40) cc_final: 0.8475 (tp-100) REVERT: B 170 TYR cc_start: 0.8692 (t80) cc_final: 0.8344 (t80) REVERT: B 260 LEU cc_start: 0.8125 (mt) cc_final: 0.7851 (mt) REVERT: B 770 ILE cc_start: 0.8935 (mt) cc_final: 0.8656 (mm) REVERT: B 842 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8048 (tpp-160) REVERT: B 1003 GLN cc_start: 0.9062 (tp40) cc_final: 0.8474 (tp-100) REVERT: C 170 TYR cc_start: 0.8694 (t80) cc_final: 0.8345 (t80) REVERT: C 260 LEU cc_start: 0.8127 (mt) cc_final: 0.7851 (mt) REVERT: C 770 ILE cc_start: 0.8934 (mt) cc_final: 0.8656 (mm) REVERT: C 842 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8048 (tpp-160) REVERT: C 1003 GLN cc_start: 0.9060 (tp40) cc_final: 0.8474 (tp-100) REVERT: D 170 TYR cc_start: 0.8693 (t80) cc_final: 0.8345 (t80) REVERT: D 260 LEU cc_start: 0.8129 (mt) cc_final: 0.7854 (mt) REVERT: D 770 ILE cc_start: 0.8935 (mt) cc_final: 0.8656 (mm) REVERT: D 842 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8048 (tpp-160) REVERT: D 1003 GLN cc_start: 0.9061 (tp40) cc_final: 0.8473 (tp-100) outliers start: 60 outliers final: 56 residues processed: 392 average time/residue: 0.7422 time to fit residues: 477.1480 Evaluate side-chains 408 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 VAL Chi-restraints excluded: chain B residue 1050 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1050 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 835 ASP Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 870 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1050 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS B 259 HIS C 259 HIS D 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106608 restraints weight = 148345.911| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.06 r_work: 0.3268 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26643 Z= 0.200 Angle : 0.463 5.896 36358 Z= 0.248 Chirality : 0.034 0.144 4323 Planarity : 0.004 0.054 4496 Dihedral : 6.178 62.414 3820 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.22 % Allowed : 15.66 % Favored : 82.12 % 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: 2.44 (0.15), residues: 3404 helix: 2.55 (0.11), residues: 2464 sheet: -0.40 (0.35), residues: 176 loop : -1.12 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 877 HIS 0.007 0.001 HIS C 500 PHE 0.010 0.001 PHE C 809 TYR 0.007 0.001 TYR B 506 ARG 0.004 0.000 ARG C 829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10512.13 seconds wall clock time: 186 minutes 41.07 seconds (11201.07 seconds total)