Starting phenix.real_space_refine on Fri Apr 5 13:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/04_2024/8e4q_27896_neut_trim_updated.pdb" } resolution = 3.51 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= 0.012 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 128 5.16 5 C 18040 2.51 5 N 4516 2.21 5 O 4776 1.98 5 H 25664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 53136 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "B" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "D" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "C" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 18.05, per 1000 atoms: 0.34 Number of scatterers: 53136 At special positions: 0 Unit cell: (156.6, 156.6, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 12 15.00 O 4776 8.00 N 4516 7.00 C 18040 6.00 H 25664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=1.39 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A1042 " distance=1.76 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=1.39 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B1042 " distance=1.76 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=1.39 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D1042 " distance=1.77 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=1.39 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C1042 " distance=1.76 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: 30.59 Conformation dependent library (CDL) restraints added in 4.3 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 4 sheets defined 66.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.91 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.801A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 removed outlier: 5.494A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.182A 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 498 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.511A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 666 through 670 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 707 Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR A 732 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 797 through 818 removed outlier: 4.059A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE A 899 " --> pdb=" O TRP A 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE A1016 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1102 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.802A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.805A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 5.495A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.183A 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 498 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.511A pdb=" N ILE B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.530A pdb=" N GLU B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 666 through 670 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 707 Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR B 732 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN B 785 " --> pdb=" O ASP B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 797 through 818 removed outlier: 4.058A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.698A pdb=" N PHE B 899 " --> pdb=" O TRP B 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B 981 " --> pdb=" O MET B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP B 993 " --> pdb=" O ASN B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE B1016 " --> pdb=" O PRO B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE B1051 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1068 " --> pdb=" O VAL B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1102 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.800A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 368' Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU D 433 " --> pdb=" O GLN D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP D 444 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 removed outlier: 5.494A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.182A 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 498 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.510A pdb=" N ILE D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 666 through 670 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 707 Processing helix chain 'D' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR D 732 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN D 785 " --> pdb=" O ASP D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 795 No H-bonds generated for 'chain 'D' and resid 793 through 795' Processing helix chain 'D' and resid 797 through 818 removed outlier: 4.059A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER D 826 " --> pdb=" O SER D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE D 899 " --> pdb=" O TRP D 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 900 " --> pdb=" O GLU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 910 Processing helix chain 'D' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR D 980 " --> pdb=" O ALA D 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR D 981 " --> pdb=" O MET D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1007 removed outlier: 3.847A pdb=" N TRP D 993 " --> pdb=" O ASN D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE D1016 " --> pdb=" O PRO D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE D1051 " --> pdb=" O GLU D1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D1068 " --> pdb=" O VAL D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1102 Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.801A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 426 through 435 removed outlier: 3.519A pdb=" N LEU C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 removed outlier: 5.495A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.182A 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 498 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 532 removed outlier: 3.780A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.510A pdb=" N ILE C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 666 through 670 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 707 Processing helix chain 'C' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR C 732 " --> pdb=" O SER C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN C 785 " --> pdb=" O ASP C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 795 No H-bonds generated for 'chain 'C' and resid 793 through 795' Processing helix chain 'C' and resid 797 through 818 removed outlier: 4.060A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 851 removed outlier: 3.618A pdb=" N SER C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 910 Processing helix chain 'C' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR C 981 " --> pdb=" O MET C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE C1016 " --> pdb=" O PRO C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C1068 " --> pdb=" O VAL C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1102 Processing sheet with id= A, first strand: chain 'A' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 148 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 304 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 148 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 304 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 148 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 304 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL C 148 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 304 " --> pdb=" O VAL C 148 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4476 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: 16.18 Time building geometry restraints manager: 32.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25616 1.02 - 1.22: 122 1.22 - 1.43: 12023 1.43 - 1.63: 15811 1.63 - 1.83: 208 Bond restraints: 53780 Sorted by residual: bond pdb=" CA ILE A 956 " pdb=" CB ILE A 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE C 956 " pdb=" CB ILE C 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE B 956 " pdb=" CB ILE B 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE D 956 " pdb=" CB ILE D 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" C HIS D 559 " pdb=" O HIS D 559 " ideal model delta sigma weight residual 1.235 1.221 0.014 4.70e-03 4.53e+04 8.62e+00 ... (remaining 53775 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.95: 436 105.95 - 112.98: 60081 112.98 - 120.01: 16550 120.01 - 127.03: 19076 127.03 - 134.06: 349 Bond angle restraints: 96492 Sorted by residual: angle pdb=" C ILE A 408 " pdb=" CA ILE A 408 " pdb=" CB ILE A 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE D 408 " pdb=" CA ILE D 408 " pdb=" CB ILE D 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE C 408 " pdb=" CA ILE C 408 " pdb=" CB ILE C 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE B 408 " pdb=" CA ILE B 408 " pdb=" CB ILE B 408 " ideal model delta sigma weight residual 111.97 107.40 4.57 1.28e+00 6.10e-01 1.27e+01 angle pdb=" N VAL C 302 " pdb=" CA VAL C 302 " pdb=" C VAL C 302 " ideal model delta sigma weight residual 108.46 113.73 -5.27 1.49e+00 4.50e-01 1.25e+01 ... (remaining 96487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 23493 17.67 - 35.35: 1586 35.35 - 53.02: 444 53.02 - 70.70: 133 70.70 - 88.37: 12 Dihedral angle restraints: 25668 sinusoidal: 12708 harmonic: 12960 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 326 " pdb=" CB CYS B 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.99 56.99 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS C 303 " pdb=" SG CYS C 303 " pdb=" SG CYS C 326 " pdb=" CB CYS C 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.95 56.95 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS D 303 " pdb=" SG CYS D 303 " pdb=" SG CYS D 326 " pdb=" CB CYS D 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.90 56.90 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 25665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3722 0.051 - 0.102: 637 0.102 - 0.153: 109 0.153 - 0.204: 4 0.204 - 0.255: 4 Chirality restraints: 4476 Sorted by residual: chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE A 301 " pdb=" N ILE A 301 " pdb=" C ILE A 301 " pdb=" CB ILE A 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE D 301 " pdb=" N ILE D 301 " pdb=" C ILE D 301 " pdb=" CB ILE D 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 4473 not shown) Planarity restraints: 8132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 510 " -0.048 2.00e-02 2.50e+03 5.14e-02 3.97e+01 pdb=" CD GLN D 510 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN D 510 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN D 510 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN D 510 " -0.076 2.00e-02 2.50e+03 pdb="HE22 GLN D 510 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 510 " 0.048 2.00e-02 2.50e+03 5.14e-02 3.96e+01 pdb=" CD GLN B 510 " -0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN B 510 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN B 510 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 510 " 0.076 2.00e-02 2.50e+03 pdb="HE22 GLN B 510 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 510 " -0.048 2.00e-02 2.50e+03 5.14e-02 3.96e+01 pdb=" CD GLN A 510 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN A 510 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN A 510 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 510 " -0.076 2.00e-02 2.50e+03 pdb="HE22 GLN A 510 " 0.075 2.00e-02 2.50e+03 ... (remaining 8129 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1742 2.15 - 2.76: 95320 2.76 - 3.38: 142253 3.38 - 3.99: 167114 3.99 - 4.60: 272761 Nonbonded interactions: 679190 Sorted by model distance: nonbonded pdb="HD11 ILE C 146 " pdb=" HE ARG C 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE A 146 " pdb=" HE ARG A 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE D 146 " pdb=" HE ARG D 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE B 146 " pdb=" HE ARG B 278 " model vdw 1.540 2.270 nonbonded pdb="HG11 VAL B 775 " pdb=" HD2 PHE B 809 " model vdw 1.578 2.270 ... (remaining 679185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.630 Extract box with map and model: 5.780 Check model and map are aligned: 0.720 Set scattering table: 0.390 Process input model: 124.480 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28116 Z= 0.272 Angle : 0.622 6.568 38288 Z= 0.363 Chirality : 0.040 0.255 4476 Planarity : 0.004 0.053 4696 Dihedral : 12.904 77.452 9368 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.15 % Allowed : 9.53 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3456 helix: 1.88 (0.10), residues: 2344 sheet: -0.29 (0.36), residues: 184 loop : -1.82 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 824 HIS 0.003 0.001 HIS C 389 PHE 0.013 0.001 PHE A 998 TYR 0.013 0.001 TYR C 904 ARG 0.004 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 395 time to evaluate : 3.117 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: A 614 SER cc_start: 0.8867 (t) cc_final: 0.8582 (p) REVERT: B 614 SER cc_start: 0.8886 (t) cc_final: 0.8582 (p) REVERT: D 614 SER cc_start: 0.8897 (t) cc_final: 0.8586 (p) REVERT: D 781 ASP cc_start: 0.8255 (t0) cc_final: 0.7739 (t0) REVERT: C 614 SER cc_start: 0.8843 (t) cc_final: 0.8582 (p) REVERT: C 781 ASP cc_start: 0.8254 (t0) cc_final: 0.7737 (t0) outliers start: 4 outliers final: 0 residues processed: 395 average time/residue: 0.6980 time to fit residues: 436.0576 Evaluate side-chains 219 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 GLN B 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28116 Z= 0.311 Angle : 0.556 11.989 38288 Z= 0.311 Chirality : 0.038 0.179 4476 Planarity : 0.004 0.056 4696 Dihedral : 6.649 57.876 3876 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.25 % Allowed : 13.31 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.14), residues: 3456 helix: 2.00 (0.10), residues: 2352 sheet: -1.02 (0.36), residues: 184 loop : -1.62 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 682 HIS 0.003 0.001 HIS C 559 PHE 0.015 0.001 PHE D 809 TYR 0.011 0.001 TYR B 904 ARG 0.005 0.000 ARG D 894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 3.122 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: A 445 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 808 TYR cc_start: 0.8013 (m-80) cc_final: 0.7559 (m-10) REVERT: B 445 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7101 (mt-10) REVERT: B 808 TYR cc_start: 0.7957 (m-80) cc_final: 0.7485 (m-10) REVERT: D 445 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7111 (mt-10) REVERT: D 808 TYR cc_start: 0.8017 (m-80) cc_final: 0.7542 (m-10) REVERT: C 445 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7109 (mt-10) REVERT: C 808 TYR cc_start: 0.8026 (m-80) cc_final: 0.7543 (m-10) outliers start: 33 outliers final: 12 residues processed: 257 average time/residue: 0.6134 time to fit residues: 260.1259 Evaluate side-chains 230 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 28116 Z= 0.365 Angle : 0.543 5.513 38288 Z= 0.307 Chirality : 0.037 0.145 4476 Planarity : 0.004 0.044 4696 Dihedral : 6.602 61.919 3876 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.89 % Allowed : 13.31 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 3456 helix: 2.01 (0.10), residues: 2348 sheet: -1.50 (0.35), residues: 184 loop : -1.79 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 682 HIS 0.003 0.001 HIS C 559 PHE 0.012 0.001 PHE A 629 TYR 0.013 0.001 TYR D 787 ARG 0.006 0.001 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 3.305 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: A 445 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 808 TYR cc_start: 0.8005 (m-80) cc_final: 0.7492 (m-10) REVERT: B 445 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7223 (mt-10) REVERT: B 496 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 808 TYR cc_start: 0.8017 (m-80) cc_final: 0.7491 (m-10) REVERT: D 445 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7221 (mt-10) REVERT: D 496 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8732 (mp) REVERT: D 808 TYR cc_start: 0.8009 (m-80) cc_final: 0.7501 (m-10) REVERT: C 445 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 496 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 808 TYR cc_start: 0.8002 (m-80) cc_final: 0.7481 (m-10) outliers start: 50 outliers final: 25 residues processed: 268 average time/residue: 0.6066 time to fit residues: 270.2099 Evaluate side-chains 224 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28116 Z= 0.212 Angle : 0.486 7.650 38288 Z= 0.267 Chirality : 0.035 0.132 4476 Planarity : 0.004 0.053 4696 Dihedral : 6.284 58.950 3876 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.91 % Allowed : 15.02 % Favored : 84.08 % 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: 1.73 (0.14), residues: 3456 helix: 2.40 (0.10), residues: 2356 sheet: -1.77 (0.33), residues: 180 loop : -1.67 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 824 HIS 0.002 0.001 HIS C 389 PHE 0.010 0.001 PHE B 809 TYR 0.011 0.001 TYR A 904 ARG 0.006 0.000 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 3.134 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 445 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 496 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8738 (mp) REVERT: A 808 TYR cc_start: 0.8080 (m-80) cc_final: 0.7476 (m-10) REVERT: B 445 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 495 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 496 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8695 (mp) REVERT: B 808 TYR cc_start: 0.7946 (m-80) cc_final: 0.7418 (m-10) REVERT: D 445 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7466 (mt-10) REVERT: D 495 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 496 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8691 (mp) REVERT: D 808 TYR cc_start: 0.8058 (m-80) cc_final: 0.7461 (m-10) REVERT: C 445 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 495 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 496 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8697 (mp) REVERT: C 808 TYR cc_start: 0.8082 (m-80) cc_final: 0.7470 (m-10) outliers start: 24 outliers final: 12 residues processed: 234 average time/residue: 0.5942 time to fit residues: 234.2842 Evaluate side-chains 216 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 28116 Z= 0.310 Angle : 0.513 7.519 38288 Z= 0.286 Chirality : 0.036 0.181 4476 Planarity : 0.004 0.046 4696 Dihedral : 6.366 61.799 3876 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.70 % Allowed : 14.64 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.14), residues: 3456 helix: 2.30 (0.10), residues: 2356 sheet: -1.88 (0.34), residues: 180 loop : -1.69 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 682 HIS 0.003 0.001 HIS C 559 PHE 0.011 0.001 PHE B 629 TYR 0.012 0.001 TYR B 787 ARG 0.005 0.000 ARG A 861 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 3.130 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 445 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 496 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 592 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 808 TYR cc_start: 0.8166 (m-80) cc_final: 0.7563 (m-10) REVERT: B 445 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 495 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 496 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 592 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 808 TYR cc_start: 0.8141 (m-80) cc_final: 0.7546 (m-10) REVERT: D 445 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7490 (mt-10) REVERT: D 495 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 496 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8558 (mp) REVERT: D 592 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8734 (mp) REVERT: D 808 TYR cc_start: 0.8157 (m-80) cc_final: 0.7554 (m-10) REVERT: C 445 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 495 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 496 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 592 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 808 TYR cc_start: 0.8103 (m-80) cc_final: 0.7539 (m-10) outliers start: 45 outliers final: 21 residues processed: 247 average time/residue: 0.5700 time to fit residues: 239.0756 Evaluate side-chains 219 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 chunk 344 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 972 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28116 Z= 0.204 Angle : 0.485 8.192 38288 Z= 0.265 Chirality : 0.036 0.176 4476 Planarity : 0.003 0.048 4696 Dihedral : 6.204 60.439 3876 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.87 % Allowed : 15.51 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.14), residues: 3456 helix: 2.50 (0.11), residues: 2360 sheet: -1.79 (0.35), residues: 176 loop : -1.71 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 993 HIS 0.002 0.001 HIS C 559 PHE 0.010 0.001 PHE C 629 TYR 0.010 0.001 TYR A 904 ARG 0.005 0.000 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 3.140 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: A 445 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 496 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 592 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 808 TYR cc_start: 0.8077 (m-80) cc_final: 0.7563 (m-10) REVERT: B 445 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 496 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 592 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 808 TYR cc_start: 0.8135 (m-80) cc_final: 0.7521 (m-10) REVERT: D 445 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 496 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 592 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8710 (mp) REVERT: D 808 TYR cc_start: 0.8088 (m-80) cc_final: 0.7584 (m-10) REVERT: C 445 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 496 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8549 (mp) REVERT: C 592 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8708 (mp) REVERT: C 808 TYR cc_start: 0.8086 (m-80) cc_final: 0.7582 (m-10) outliers start: 23 outliers final: 13 residues processed: 226 average time/residue: 0.5742 time to fit residues: 222.9928 Evaluate side-chains 222 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 972 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 343 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 GLN C 972 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 28116 Z= 0.256 Angle : 0.485 6.531 38288 Z= 0.268 Chirality : 0.036 0.167 4476 Planarity : 0.003 0.049 4696 Dihedral : 6.198 61.174 3876 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.29 % Allowed : 15.70 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.15), residues: 3456 helix: 2.48 (0.11), residues: 2360 sheet: -1.77 (0.35), residues: 176 loop : -1.73 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 993 HIS 0.002 0.001 HIS B 559 PHE 0.010 0.001 PHE B 809 TYR 0.010 0.001 TYR A 904 ARG 0.003 0.000 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 3.126 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 445 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 496 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 592 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8720 (mp) REVERT: A 808 TYR cc_start: 0.8100 (m-80) cc_final: 0.7569 (m-10) REVERT: B 445 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 496 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 592 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 808 TYR cc_start: 0.8101 (m-80) cc_final: 0.7563 (m-10) REVERT: D 445 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7478 (mt-10) REVERT: D 496 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 592 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8722 (mp) REVERT: D 808 TYR cc_start: 0.8090 (m-80) cc_final: 0.7544 (m-10) REVERT: C 445 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 496 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8724 (mp) REVERT: C 592 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 808 TYR cc_start: 0.8091 (m-80) cc_final: 0.7529 (m-10) outliers start: 34 outliers final: 16 residues processed: 235 average time/residue: 0.6005 time to fit residues: 243.0448 Evaluate side-chains 226 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.2980 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN B 438 GLN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28116 Z= 0.291 Angle : 0.505 7.362 38288 Z= 0.281 Chirality : 0.036 0.174 4476 Planarity : 0.004 0.055 4696 Dihedral : 6.219 62.942 3876 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.32 % Allowed : 16.00 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3456 helix: 2.46 (0.11), residues: 2360 sheet: -1.77 (0.36), residues: 176 loop : -1.75 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 682 HIS 0.002 0.001 HIS D 559 PHE 0.023 0.001 PHE A 911 TYR 0.011 0.001 TYR C 904 ARG 0.004 0.000 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 3.139 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: A 496 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 592 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 808 TYR cc_start: 0.8130 (m-80) cc_final: 0.7591 (m-10) REVERT: B 496 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 592 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 808 TYR cc_start: 0.8096 (m-80) cc_final: 0.7568 (m-10) REVERT: D 496 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8637 (mp) REVERT: D 592 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8716 (mp) REVERT: D 808 TYR cc_start: 0.8130 (m-80) cc_final: 0.7587 (m-10) REVERT: C 496 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 592 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8735 (mp) REVERT: C 808 TYR cc_start: 0.8135 (m-80) cc_final: 0.7593 (m-10) outliers start: 35 outliers final: 24 residues processed: 232 average time/residue: 0.5827 time to fit residues: 230.3305 Evaluate side-chains 226 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN D 429 GLN C 429 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28116 Z= 0.248 Angle : 0.485 6.143 38288 Z= 0.269 Chirality : 0.036 0.156 4476 Planarity : 0.004 0.053 4696 Dihedral : 6.169 62.590 3876 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.10 % Allowed : 16.38 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.15), residues: 3456 helix: 2.52 (0.11), residues: 2348 sheet: -1.77 (0.36), residues: 176 loop : -1.77 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 993 HIS 0.002 0.001 HIS B 559 PHE 0.020 0.001 PHE B 911 TYR 0.010 0.001 TYR A 904 ARG 0.004 0.000 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 3.183 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 496 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 592 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 808 TYR cc_start: 0.8122 (m-80) cc_final: 0.7576 (m-10) REVERT: B 496 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 592 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 808 TYR cc_start: 0.8098 (m-80) cc_final: 0.7595 (m-10) REVERT: D 496 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 592 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (mp) REVERT: D 808 TYR cc_start: 0.8127 (m-80) cc_final: 0.7585 (m-10) REVERT: C 496 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 592 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8729 (mp) REVERT: C 808 TYR cc_start: 0.8130 (m-80) cc_final: 0.7589 (m-10) outliers start: 29 outliers final: 21 residues processed: 227 average time/residue: 0.5926 time to fit residues: 230.3653 Evaluate side-chains 223 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 282 optimal weight: 50.0000 chunk 29 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28116 Z= 0.328 Angle : 0.517 6.052 38288 Z= 0.288 Chirality : 0.036 0.162 4476 Planarity : 0.004 0.054 4696 Dihedral : 6.252 65.235 3876 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.21 % Allowed : 16.38 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.14), residues: 3456 helix: 2.39 (0.11), residues: 2352 sheet: -1.79 (0.36), residues: 176 loop : -1.81 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 682 HIS 0.003 0.001 HIS B 559 PHE 0.019 0.001 PHE B 911 TYR 0.011 0.001 TYR D 904 ARG 0.004 0.000 ARG C 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 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 VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 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 VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 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 SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 3.443 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: A 496 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 592 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 808 TYR cc_start: 0.8090 (m-80) cc_final: 0.7646 (m-10) REVERT: B 496 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8626 (mp) REVERT: B 592 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 808 TYR cc_start: 0.8129 (m-80) cc_final: 0.7626 (m-10) REVERT: D 496 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8624 (mp) REVERT: D 592 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8711 (mp) REVERT: D 808 TYR cc_start: 0.8134 (m-80) cc_final: 0.7660 (m-10) REVERT: C 496 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8626 (mp) REVERT: C 592 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 808 TYR cc_start: 0.8139 (m-80) cc_final: 0.7661 (m-10) outliers start: 32 outliers final: 23 residues processed: 223 average time/residue: 0.6032 time to fit residues: 231.0038 Evaluate side-chains 224 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 858 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089701 restraints weight = 168004.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093590 restraints weight = 77272.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096082 restraints weight = 49568.015| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28116 Z= 0.189 Angle : 0.478 9.905 38288 Z= 0.260 Chirality : 0.035 0.146 4476 Planarity : 0.003 0.049 4696 Dihedral : 6.064 61.784 3876 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.91 % Allowed : 16.45 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.15), residues: 3456 helix: 2.66 (0.11), residues: 2348 sheet: -1.82 (0.35), residues: 176 loop : -1.81 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 993 HIS 0.002 0.001 HIS A 136 PHE 0.020 0.001 PHE B 911 TYR 0.009 0.001 TYR A 904 ARG 0.003 0.000 ARG C 861 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6433.80 seconds wall clock time: 112 minutes 36.17 seconds (6756.17 seconds total)