Starting phenix.real_space_refine on Sat Apr 6 00:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4l_27891/04_2024/8e4l_27891_neut_trim_updated.pdb" } resolution = 3.32 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= 0.004 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 16 5.49 5 S 108 5.16 5 C 18328 2.51 5 N 4572 2.21 5 O 4948 1.98 5 H 26580 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 54556 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "B" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "C" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "D" Number of atoms: 13568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 13568 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 21, 'TRANS': 876} Chain breaks: 10 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 281 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'PIO': 1, 'UL9': 1, 'ULO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 18.06, per 1000 atoms: 0.33 Number of scatterers: 54556 At special positions: 0 Unit cell: (152.28, 152.28, 144.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 16 15.00 O 4948 8.00 N 4572 7.00 C 18328 6.00 H 26580 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.90 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.90 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.90 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.90 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: 31.14 Conformation dependent library (CDL) restraints added in 4.2 seconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 4 sheets defined 67.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.77 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.816A pdb=" N ILE A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 656 through 662 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 701 removed outlier: 3.611A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 No H-bonds generated for 'chain 'A' and resid 727 through 730' Processing helix chain 'A' and resid 734 through 757 Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 797 through 818 Processing helix chain 'A' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 889 Proline residue: A 855 - end of helix removed outlier: 3.988A pdb=" N ILE A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 873 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 913 removed outlier: 3.745A pdb=" N ILE A 899 " --> pdb=" O ARG A 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 903 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) Proline residue: A 907 - end of helix removed outlier: 4.535A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 968 through 988 Processing helix chain 'A' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN A1074 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.815A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS B 357 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 656 through 662 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 701 removed outlier: 3.611A pdb=" N PHE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 730 No H-bonds generated for 'chain 'B' and resid 727 through 730' Processing helix chain 'B' and resid 734 through 757 Processing helix chain 'B' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 797 through 818 Processing helix chain 'B' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG B 842 " --> pdb=" O ILE B 838 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 889 Proline residue: B 855 - end of helix removed outlier: 3.988A pdb=" N ILE B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE B 872 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 873 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 913 removed outlier: 3.745A pdb=" N ILE B 899 " --> pdb=" O ARG B 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 903 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 906 " --> pdb=" O SER B 902 " (cutoff:3.500A) Proline residue: B 907 - end of helix removed outlier: 4.535A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 951 through 964 removed outlier: 4.041A pdb=" N ILE B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 968 through 988 Processing helix chain 'B' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN B1074 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B1075 " --> pdb=" O ALA B1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.816A pdb=" N ILE C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 165 " --> pdb=" O MET C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 351 through 361 removed outlier: 4.141A pdb=" N LYS C 357 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 371 through 386 removed outlier: 3.841A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 removed outlier: 4.179A pdb=" N ILE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 3.641A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 532 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.627A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.561A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 644 Processing helix chain 'C' and resid 656 through 662 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 701 removed outlier: 3.611A pdb=" N PHE C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 730 No H-bonds generated for 'chain 'C' and resid 727 through 730' Processing helix chain 'C' and resid 734 through 757 Processing helix chain 'C' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 797 through 818 Processing helix chain 'C' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG C 842 " --> pdb=" O ILE C 838 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 889 Proline residue: C 855 - end of helix removed outlier: 3.988A pdb=" N ILE C 858 " --> pdb=" O GLY C 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 872 " --> pdb=" O PHE C 868 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 873 " --> pdb=" O PHE C 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 913 removed outlier: 3.744A pdb=" N ILE C 899 " --> pdb=" O ARG C 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 903 " --> pdb=" O ILE C 899 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Proline residue: C 907 - end of helix removed outlier: 4.535A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 922 Processing helix chain 'C' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE C 957 " --> pdb=" O GLU C 953 " (cutoff:3.500A) Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 968 through 988 Processing helix chain 'C' and resid 993 through 1006 removed outlier: 3.916A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1103 removed outlier: 4.152A pdb=" N ASN C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C1075 " --> pdb=" O ALA C1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG C1079 " --> pdb=" O SER C1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.815A pdb=" N ILE D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 351 through 361 removed outlier: 4.142A pdb=" N LYS D 357 " --> pdb=" O MET D 353 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU D 358 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.840A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 4.178A pdb=" N ILE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 409 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 424 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 3.642A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.626A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.560A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 656 through 662 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 701 removed outlier: 3.611A pdb=" N PHE D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 730 No H-bonds generated for 'chain 'D' and resid 727 through 730' Processing helix chain 'D' and resid 734 through 757 Processing helix chain 'D' and resid 765 through 788 removed outlier: 3.891A pdb=" N LEU D 771 " --> pdb=" O PRO D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 795 No H-bonds generated for 'chain 'D' and resid 792 through 795' Processing helix chain 'D' and resid 797 through 818 Processing helix chain 'D' and resid 822 through 847 removed outlier: 3.573A pdb=" N ARG D 842 " --> pdb=" O ILE D 838 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 889 Proline residue: D 855 - end of helix removed outlier: 3.988A pdb=" N ILE D 858 " --> pdb=" O GLY D 854 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 872 " --> pdb=" O PHE D 868 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 873 " --> pdb=" O PHE D 869 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 913 removed outlier: 3.744A pdb=" N ILE D 899 " --> pdb=" O ARG D 895 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 903 " --> pdb=" O ILE D 899 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR D 905 " --> pdb=" O ARG D 901 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Proline residue: D 907 - end of helix removed outlier: 4.535A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 922 Processing helix chain 'D' and resid 951 through 964 removed outlier: 4.040A pdb=" N ILE D 957 " --> pdb=" O GLU D 953 " (cutoff:3.500A) Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 968 through 988 Processing helix chain 'D' and resid 993 through 1006 removed outlier: 3.915A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS D1006 " --> pdb=" O VAL D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1027 removed outlier: 4.400A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1103 removed outlier: 4.153A pdb=" N ASN D1074 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER D1075 " --> pdb=" O ALA D1071 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG D1079 " --> pdb=" O SER D1075 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS A 259 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA A 305 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 327 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS B 259 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA B 305 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 327 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS C 259 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA C 305 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 327 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.593A pdb=" N HIS D 259 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA D 305 " --> pdb=" O PRO D 325 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 327 " --> pdb=" O ALA D 305 " (cutoff:3.500A) 1624 hydrogen bonds defined for protein. 4728 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: 17.12 Time building geometry restraints manager: 33.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 26540 1.03 - 1.24: 2867 1.24 - 1.45: 9624 1.45 - 1.65: 15953 1.65 - 1.86: 192 Bond restraints: 55176 Sorted by residual: bond pdb=" C05 UL9 C1202 " pdb=" S06 UL9 C1202 " ideal model delta sigma weight residual 1.640 1.806 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C05 UL9 A1202 " pdb=" S06 UL9 A1202 " ideal model delta sigma weight residual 1.640 1.806 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C05 UL9 B1202 " pdb=" S06 UL9 B1202 " ideal model delta sigma weight residual 1.640 1.806 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C05 UL9 D1202 " pdb=" S06 UL9 D1202 " ideal model delta sigma weight residual 1.640 1.805 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C02 UL9 C1202 " pdb=" C03 UL9 C1202 " ideal model delta sigma weight residual 1.567 1.707 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 55171 not shown) Histogram of bond angle deviations from ideal: 100.10 - 116.06: 68916 116.06 - 132.02: 30188 132.02 - 147.98: 88 147.98 - 163.94: 0 163.94 - 179.89: 4 Bond angle restraints: 99196 Sorted by residual: angle pdb=" N MET C 859 " pdb=" CA MET C 859 " pdb=" C MET C 859 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N MET D 859 " pdb=" CA MET D 859 " pdb=" C MET D 859 " ideal model delta sigma weight residual 111.36 105.57 5.79 1.09e+00 8.42e-01 2.82e+01 angle pdb=" N MET A 859 " pdb=" CA MET A 859 " pdb=" C MET A 859 " ideal model delta sigma weight residual 111.36 105.57 5.79 1.09e+00 8.42e-01 2.82e+01 angle pdb=" N MET B 859 " pdb=" CA MET B 859 " pdb=" C MET B 859 " ideal model delta sigma weight residual 111.36 105.57 5.79 1.09e+00 8.42e-01 2.82e+01 angle pdb=" N ILE A 969 " pdb=" CA ILE A 969 " pdb=" C ILE A 969 " ideal model delta sigma weight residual 110.62 107.20 3.42 1.02e+00 9.61e-01 1.13e+01 ... (remaining 99191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 23763 14.28 - 28.56: 1653 28.56 - 42.85: 384 42.85 - 57.13: 296 57.13 - 71.41: 56 Dihedral angle restraints: 26152 sinusoidal: 13252 harmonic: 12900 Sorted by residual: 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 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+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 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 303 " pdb=" SG CYS A 303 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -19.91 -66.09 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 26149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3374 0.036 - 0.071: 811 0.071 - 0.107: 264 0.107 - 0.143: 63 0.143 - 0.179: 12 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA VAL B 972 " pdb=" N VAL B 972 " pdb=" C VAL B 972 " pdb=" CB VAL B 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA VAL A 972 " pdb=" N VAL A 972 " pdb=" C VAL A 972 " pdb=" CB VAL A 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA VAL C 972 " pdb=" N VAL C 972 " pdb=" C VAL C 972 " pdb=" CB VAL C 972 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 4521 not shown) Planarity restraints: 8252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 973 " -0.116 2.00e-02 2.50e+03 1.13e-01 1.93e+02 pdb=" CG ASN D 973 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN D 973 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN D 973 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN D 973 " -0.163 2.00e-02 2.50e+03 pdb="HD22 ASN D 973 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 973 " -0.115 2.00e-02 2.50e+03 1.13e-01 1.92e+02 pdb=" CG ASN A 973 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 973 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN A 973 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 973 " -0.163 2.00e-02 2.50e+03 pdb="HD22 ASN A 973 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 973 " -0.115 2.00e-02 2.50e+03 1.13e-01 1.92e+02 pdb=" CG ASN B 973 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 973 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN B 973 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 973 " -0.163 2.00e-02 2.50e+03 pdb="HD22 ASN B 973 " 0.157 2.00e-02 2.50e+03 ... (remaining 8249 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1231 2.12 - 2.74: 95933 2.74 - 3.36: 152995 3.36 - 3.98: 180695 3.98 - 4.60: 291946 Nonbonded interactions: 722800 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 605 " pdb=" O41 PIO D1204 " model vdw 1.506 1.850 nonbonded pdb=" HZ1 LYS D 605 " pdb=" O41 PIO C1204 " model vdw 1.586 1.850 nonbonded pdb=" O LEU C 120 " pdb=" H ASP C 264 " model vdw 1.589 1.850 nonbonded pdb=" O LEU A 120 " pdb=" H ASP A 264 " model vdw 1.589 1.850 nonbonded pdb=" O LEU D 120 " pdb=" H ASP D 264 " model vdw 1.589 1.850 ... (remaining 722795 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.610 Extract box with map and model: 5.440 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 130.270 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.210 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 0.166 28596 Z= 0.279 Angle : 0.517 5.819 38896 Z= 0.300 Chirality : 0.038 0.179 4524 Planarity : 0.003 0.025 4788 Dihedral : 11.163 71.412 9748 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.14), residues: 3504 helix: 2.55 (0.11), residues: 2444 sheet: -0.11 (0.40), residues: 196 loop : -0.91 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 436 HIS 0.003 0.001 HIS B 257 PHE 0.011 0.001 PHE A 361 TYR 0.010 0.001 TYR C 999 ARG 0.002 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 586 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 586 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 770 ILE cc_start: 0.8970 (mt) cc_final: 0.8759 (tp) REVERT: A 793 TYR cc_start: 0.8115 (t80) cc_final: 0.7725 (t80) REVERT: A 866 ASP cc_start: 0.8937 (t0) cc_final: 0.8375 (t0) REVERT: A 885 ARG cc_start: 0.8765 (mtm180) cc_final: 0.8391 (tmm-80) REVERT: A 973 ASN cc_start: 0.8874 (m-40) cc_final: 0.8585 (m110) REVERT: A 1059 MET cc_start: 0.9046 (mmm) cc_final: 0.8756 (mmm) REVERT: B 700 PHE cc_start: 0.9028 (m-80) cc_final: 0.8824 (m-80) REVERT: B 866 ASP cc_start: 0.8910 (t0) cc_final: 0.8506 (t0) REVERT: B 874 PHE cc_start: 0.8773 (t80) cc_final: 0.8465 (t80) REVERT: B 1059 MET cc_start: 0.9069 (mmm) cc_final: 0.8825 (mmm) REVERT: C 700 PHE cc_start: 0.9012 (m-80) cc_final: 0.8801 (m-80) REVERT: C 793 TYR cc_start: 0.8245 (t80) cc_final: 0.7960 (t80) REVERT: C 866 ASP cc_start: 0.8911 (t0) cc_final: 0.8498 (t0) REVERT: C 874 PHE cc_start: 0.8705 (t80) cc_final: 0.8396 (t80) REVERT: C 883 VAL cc_start: 0.9084 (m) cc_final: 0.8777 (m) REVERT: C 1059 MET cc_start: 0.9067 (mmm) cc_final: 0.8821 (mmm) REVERT: D 770 ILE cc_start: 0.8986 (mt) cc_final: 0.8780 (tp) REVERT: D 793 TYR cc_start: 0.8053 (t80) cc_final: 0.7630 (t80) REVERT: D 866 ASP cc_start: 0.8933 (t0) cc_final: 0.8304 (t0) REVERT: D 885 ARG cc_start: 0.8718 (mtm180) cc_final: 0.8376 (tmm-80) REVERT: D 973 ASN cc_start: 0.8960 (m-40) cc_final: 0.8625 (m110) REVERT: D 1059 MET cc_start: 0.9030 (mmm) cc_final: 0.8774 (mmm) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.7467 time to fit residues: 686.0389 Evaluate side-chains 316 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 3.437 ------------------------------------------------------------------------------- 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: 20.0000 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 92 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 973 ASN A 997 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 GLN B 973 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN C 973 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 GLN D 973 ASN D 997 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 28596 Z= 0.298 Angle : 0.544 7.362 38896 Z= 0.294 Chirality : 0.037 0.143 4524 Planarity : 0.003 0.027 4788 Dihedral : 7.480 65.868 3944 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.23 % Allowed : 11.97 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.14), residues: 3504 helix: 2.47 (0.10), residues: 2428 sheet: -0.36 (0.38), residues: 196 loop : -0.97 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 426 HIS 0.003 0.001 HIS D 259 PHE 0.015 0.001 PHE A 809 TYR 0.012 0.001 TYR A 772 ARG 0.003 0.000 ARG A1079 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 336 time to evaluate : 3.229 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: A 793 TYR cc_start: 0.8155 (t80) cc_final: 0.7761 (t80) REVERT: A 885 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8401 (tmm-80) REVERT: B 158 LYS cc_start: 0.7998 (tttp) cc_final: 0.7569 (mttp) REVERT: B 700 PHE cc_start: 0.9026 (m-80) cc_final: 0.8822 (m-80) REVERT: B 750 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9126 (mp) REVERT: B 793 TYR cc_start: 0.7984 (t80) cc_final: 0.7546 (t80) REVERT: B 874 PHE cc_start: 0.8778 (t80) cc_final: 0.8441 (t80) REVERT: B 885 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8339 (tmm-80) REVERT: C 158 LYS cc_start: 0.7984 (tttp) cc_final: 0.7555 (mttp) REVERT: C 700 PHE cc_start: 0.9039 (m-80) cc_final: 0.8833 (m-80) REVERT: C 750 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9108 (mp) REVERT: C 793 TYR cc_start: 0.8308 (t80) cc_final: 0.8024 (t80) REVERT: C 874 PHE cc_start: 0.8735 (t80) cc_final: 0.8390 (t80) REVERT: D 458 LEU cc_start: 0.7372 (mt) cc_final: 0.7103 (mt) REVERT: D 793 TYR cc_start: 0.8137 (t80) cc_final: 0.7768 (t80) REVERT: D 866 ASP cc_start: 0.9018 (t0) cc_final: 0.8778 (t0) REVERT: D 885 ARG cc_start: 0.8730 (mtm180) cc_final: 0.8358 (tmm-80) outliers start: 34 outliers final: 20 residues processed: 359 average time/residue: 0.7102 time to fit residues: 405.8203 Evaluate side-chains 315 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 293 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 323 optimal weight: 0.0770 chunk 349 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 321 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 459 GLN D 480 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 28596 Z= 0.219 Angle : 0.515 12.120 38896 Z= 0.276 Chirality : 0.036 0.171 4524 Planarity : 0.003 0.033 4788 Dihedral : 7.446 59.699 3944 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.31 % Allowed : 12.05 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3504 helix: 2.45 (0.10), residues: 2440 sheet: -0.70 (0.38), residues: 196 loop : -0.95 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 426 HIS 0.003 0.001 HIS C 259 PHE 0.013 0.001 PHE B 629 TYR 0.012 0.001 TYR B 999 ARG 0.007 0.000 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 303 time to evaluate : 3.228 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 631 GLU cc_start: 0.8063 (tp30) cc_final: 0.7849 (tp30) REVERT: A 793 TYR cc_start: 0.8167 (t80) cc_final: 0.7810 (t80) REVERT: A 866 ASP cc_start: 0.8855 (t0) cc_final: 0.8507 (t0) REVERT: A 874 PHE cc_start: 0.8802 (t80) cc_final: 0.8557 (t80) REVERT: A 885 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8421 (tmm-80) REVERT: A 1078 MET cc_start: 0.6433 (ptt) cc_final: 0.6109 (ptp) REVERT: B 158 LYS cc_start: 0.8069 (tttp) cc_final: 0.7587 (mttp) REVERT: B 750 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9127 (mp) REVERT: B 793 TYR cc_start: 0.8010 (t80) cc_final: 0.7572 (t80) REVERT: B 885 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8355 (tmm-80) REVERT: C 158 LYS cc_start: 0.7960 (tttp) cc_final: 0.7489 (mttp) REVERT: C 750 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9124 (mp) REVERT: C 793 TYR cc_start: 0.8301 (t80) cc_final: 0.8004 (t80) REVERT: C 955 ILE cc_start: 0.8009 (mt) cc_final: 0.7789 (tp) REVERT: D 793 TYR cc_start: 0.8093 (t80) cc_final: 0.7773 (t80) REVERT: D 866 ASP cc_start: 0.8938 (t0) cc_final: 0.8436 (t0) REVERT: D 885 ARG cc_start: 0.8730 (mtm180) cc_final: 0.8355 (tmm-80) REVERT: D 973 ASN cc_start: 0.8788 (m110) cc_final: 0.8565 (m110) outliers start: 36 outliers final: 26 residues processed: 331 average time/residue: 0.6932 time to fit residues: 367.5264 Evaluate side-chains 307 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 480 ASN B 255 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN B 671 GLN C 255 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 671 GLN C 987 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 987 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 28596 Z= 0.381 Angle : 0.571 10.901 38896 Z= 0.312 Chirality : 0.037 0.148 4524 Planarity : 0.003 0.037 4788 Dihedral : 7.548 59.884 3944 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.74 % Allowed : 12.05 % Favored : 86.21 % 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: 1.51 (0.14), residues: 3504 helix: 1.96 (0.10), residues: 2424 sheet: -1.04 (0.36), residues: 196 loop : -1.24 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 682 HIS 0.006 0.001 HIS A 559 PHE 0.020 0.001 PHE C 874 TYR 0.013 0.002 TYR A 836 ARG 0.005 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 3.395 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: A 458 LEU cc_start: 0.7453 (mt) cc_final: 0.7212 (mt) REVERT: A 793 TYR cc_start: 0.8393 (t80) cc_final: 0.8080 (t80) REVERT: A 866 ASP cc_start: 0.8879 (t0) cc_final: 0.8483 (t0) REVERT: A 885 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8395 (tmm-80) REVERT: A 1078 MET cc_start: 0.6388 (ptt) cc_final: 0.6078 (ptp) REVERT: B 158 LYS cc_start: 0.8021 (tttp) cc_final: 0.7579 (mttp) REVERT: B 458 LEU cc_start: 0.7508 (mt) cc_final: 0.7276 (mt) REVERT: B 462 MET cc_start: 0.8788 (tpp) cc_final: 0.8124 (tpt) REVERT: B 750 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9107 (mp) REVERT: B 793 TYR cc_start: 0.8197 (t80) cc_final: 0.7788 (t80) REVERT: B 866 ASP cc_start: 0.8867 (t0) cc_final: 0.8511 (t0) REVERT: B 874 PHE cc_start: 0.8904 (t80) cc_final: 0.8535 (t80) REVERT: B 885 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8377 (tmm-80) REVERT: C 158 LYS cc_start: 0.8061 (tttp) cc_final: 0.7568 (mttp) REVERT: C 458 LEU cc_start: 0.7506 (mt) cc_final: 0.7273 (mt) REVERT: C 462 MET cc_start: 0.8796 (tpp) cc_final: 0.8150 (tpt) REVERT: C 750 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9116 (mp) REVERT: C 793 TYR cc_start: 0.8392 (t80) cc_final: 0.8113 (t80) REVERT: C 885 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8350 (tmm-80) REVERT: D 458 LEU cc_start: 0.7481 (mt) cc_final: 0.7041 (mp) REVERT: D 631 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 793 TYR cc_start: 0.8233 (t80) cc_final: 0.8010 (t80) REVERT: D 866 ASP cc_start: 0.8938 (t0) cc_final: 0.8462 (t0) REVERT: D 885 ARG cc_start: 0.8740 (mtm180) cc_final: 0.8333 (tmm-80) REVERT: D 973 ASN cc_start: 0.8843 (m110) cc_final: 0.8605 (m110) outliers start: 48 outliers final: 38 residues processed: 326 average time/residue: 0.6853 time to fit residues: 360.3516 Evaluate side-chains 315 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 727 TYR Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 727 TYR Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN B 459 GLN C 459 GLN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28596 Z= 0.330 Angle : 0.537 9.466 38896 Z= 0.292 Chirality : 0.037 0.142 4524 Planarity : 0.003 0.036 4788 Dihedral : 7.559 60.884 3944 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 12.99 % Favored : 85.38 % 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: 1.46 (0.14), residues: 3504 helix: 1.95 (0.10), residues: 2424 sheet: -1.10 (0.35), residues: 196 loop : -1.34 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 682 HIS 0.004 0.001 HIS C 559 PHE 0.014 0.001 PHE A 629 TYR 0.012 0.001 TYR C 999 ARG 0.004 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 3.263 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: A 458 LEU cc_start: 0.7474 (mt) cc_final: 0.7239 (mt) REVERT: A 462 MET cc_start: 0.8806 (tpp) cc_final: 0.8416 (ttt) REVERT: A 793 TYR cc_start: 0.8333 (t80) cc_final: 0.8040 (t80) REVERT: A 866 ASP cc_start: 0.8889 (t0) cc_final: 0.8483 (t0) REVERT: A 885 ARG cc_start: 0.8795 (mtm180) cc_final: 0.8429 (tmm-80) REVERT: A 1078 MET cc_start: 0.6485 (ptt) cc_final: 0.6196 (ptp) REVERT: B 750 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9146 (mp) REVERT: B 866 ASP cc_start: 0.8889 (t0) cc_final: 0.8485 (t0) REVERT: B 885 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8396 (tmm-80) REVERT: C 158 LYS cc_start: 0.7986 (tttp) cc_final: 0.7504 (mttp) REVERT: C 458 LEU cc_start: 0.7491 (mt) cc_final: 0.7259 (mt) REVERT: C 750 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9145 (mp) REVERT: C 793 TYR cc_start: 0.8380 (t80) cc_final: 0.8128 (t80) REVERT: C 866 ASP cc_start: 0.8840 (t0) cc_final: 0.8474 (t0) REVERT: C 885 ARG cc_start: 0.8799 (mtm180) cc_final: 0.8391 (tmm-80) REVERT: D 458 LEU cc_start: 0.7505 (mt) cc_final: 0.7075 (mp) REVERT: D 793 TYR cc_start: 0.8167 (t80) cc_final: 0.7913 (t80) REVERT: D 866 ASP cc_start: 0.8936 (t0) cc_final: 0.8626 (t0) REVERT: D 885 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8384 (tmm-80) REVERT: D 973 ASN cc_start: 0.8868 (m110) cc_final: 0.8636 (m110) outliers start: 45 outliers final: 37 residues processed: 317 average time/residue: 0.6663 time to fit residues: 340.9473 Evaluate side-chains 317 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 344 optimal weight: 0.8980 chunk 285 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN B 676 ASN C 676 ASN D 666 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 28596 Z= 0.141 Angle : 0.474 8.637 38896 Z= 0.247 Chirality : 0.035 0.144 4524 Planarity : 0.003 0.032 4788 Dihedral : 7.028 59.996 3944 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.16 % Allowed : 13.06 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.15), residues: 3504 helix: 2.49 (0.11), residues: 2404 sheet: -0.87 (0.36), residues: 192 loop : -1.17 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 994 HIS 0.002 0.000 HIS C 259 PHE 0.019 0.001 PHE C 731 TYR 0.014 0.001 TYR C 999 ARG 0.004 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 306 time to evaluate : 3.264 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: A 462 MET cc_start: 0.8745 (tpp) cc_final: 0.8271 (ttt) REVERT: A 793 TYR cc_start: 0.8243 (t80) cc_final: 0.7961 (t80) REVERT: A 885 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8396 (tmm-80) REVERT: A 1078 MET cc_start: 0.6299 (ptt) cc_final: 0.6011 (ptp) REVERT: B 750 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9126 (mp) REVERT: B 793 TYR cc_start: 0.8202 (t80) cc_final: 0.7829 (t80) REVERT: B 866 ASP cc_start: 0.8862 (t0) cc_final: 0.8397 (t0) REVERT: B 885 ARG cc_start: 0.8782 (mtm180) cc_final: 0.8382 (tmm-80) REVERT: C 750 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9138 (mp) REVERT: C 793 TYR cc_start: 0.8269 (t80) cc_final: 0.8025 (t80) REVERT: C 866 ASP cc_start: 0.8876 (t0) cc_final: 0.8378 (t0) REVERT: C 885 ARG cc_start: 0.8757 (mtm180) cc_final: 0.8333 (tmm-80) REVERT: D 793 TYR cc_start: 0.8157 (t80) cc_final: 0.7869 (t80) REVERT: D 866 ASP cc_start: 0.8922 (t0) cc_final: 0.8561 (t0) REVERT: D 885 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8366 (tmm-80) REVERT: D 954 TRP cc_start: 0.7484 (m-10) cc_final: 0.7105 (m100) REVERT: D 973 ASN cc_start: 0.8803 (m110) cc_final: 0.8564 (m110) outliers start: 32 outliers final: 18 residues processed: 327 average time/residue: 0.6905 time to fit residues: 364.2030 Evaluate side-chains 305 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 285 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28596 Z= 0.355 Angle : 0.546 8.782 38896 Z= 0.294 Chirality : 0.037 0.150 4524 Planarity : 0.003 0.035 4788 Dihedral : 6.950 58.826 3944 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 13.64 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.14), residues: 3504 helix: 2.11 (0.10), residues: 2424 sheet: -1.12 (0.34), residues: 196 loop : -1.25 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 682 HIS 0.005 0.001 HIS D 559 PHE 0.018 0.001 PHE C 731 TYR 0.015 0.001 TYR B 836 ARG 0.003 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 3.308 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: A 793 TYR cc_start: 0.8345 (t80) cc_final: 0.8076 (t80) REVERT: A 885 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8436 (tmm-80) REVERT: A 954 TRP cc_start: 0.7421 (m-10) cc_final: 0.6998 (m100) REVERT: A 1078 MET cc_start: 0.6374 (ptt) cc_final: 0.6091 (ptp) REVERT: B 750 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9126 (mp) REVERT: B 793 TYR cc_start: 0.8385 (t80) cc_final: 0.8072 (t80) REVERT: B 866 ASP cc_start: 0.8881 (t0) cc_final: 0.8525 (t0) REVERT: B 885 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8411 (tmm-80) REVERT: C 750 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9125 (mp) REVERT: C 793 TYR cc_start: 0.8339 (t80) cc_final: 0.8129 (t80) REVERT: C 866 ASP cc_start: 0.8903 (t0) cc_final: 0.8516 (t0) REVERT: D 793 TYR cc_start: 0.8233 (t80) cc_final: 0.8030 (t80) REVERT: D 866 ASP cc_start: 0.8951 (t0) cc_final: 0.8636 (t0) REVERT: D 885 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8362 (tmm-80) REVERT: D 973 ASN cc_start: 0.8851 (m110) cc_final: 0.8630 (m110) outliers start: 39 outliers final: 30 residues processed: 298 average time/residue: 0.6860 time to fit residues: 329.0296 Evaluate side-chains 304 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 638 ASP Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 0.4980 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN B 987 GLN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28596 Z= 0.251 Angle : 0.509 8.822 38896 Z= 0.270 Chirality : 0.036 0.151 4524 Planarity : 0.003 0.036 4788 Dihedral : 6.785 59.534 3944 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.45 % Allowed : 13.64 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.78 (0.14), residues: 3504 helix: 2.19 (0.10), residues: 2428 sheet: -0.95 (0.35), residues: 192 loop : -1.24 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 682 HIS 0.003 0.001 HIS B 259 PHE 0.020 0.001 PHE C 731 TYR 0.013 0.001 TYR D 836 ARG 0.003 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 3.286 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 793 TYR cc_start: 0.8328 (t80) cc_final: 0.8059 (t80) REVERT: A 874 PHE cc_start: 0.8926 (t80) cc_final: 0.8651 (t80) REVERT: A 885 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8393 (tmm-80) REVERT: A 1078 MET cc_start: 0.6334 (ptt) cc_final: 0.6049 (ptp) REVERT: B 750 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 793 TYR cc_start: 0.8314 (t80) cc_final: 0.8024 (t80) REVERT: B 866 ASP cc_start: 0.8893 (t0) cc_final: 0.8493 (t0) REVERT: B 874 PHE cc_start: 0.8906 (t80) cc_final: 0.8647 (t80) REVERT: C 750 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9129 (mp) REVERT: C 866 ASP cc_start: 0.8895 (t0) cc_final: 0.8490 (t0) REVERT: D 793 TYR cc_start: 0.8220 (t80) cc_final: 0.8011 (t80) REVERT: D 866 ASP cc_start: 0.8951 (t0) cc_final: 0.8583 (t0) REVERT: D 885 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8378 (tmm-80) REVERT: D 973 ASN cc_start: 0.8840 (m110) cc_final: 0.8618 (m110) outliers start: 40 outliers final: 32 residues processed: 299 average time/residue: 0.6836 time to fit residues: 332.0245 Evaluate side-chains 303 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 269 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 988 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 319 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 251 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28596 Z= 0.140 Angle : 0.475 9.448 38896 Z= 0.246 Chirality : 0.035 0.151 4524 Planarity : 0.003 0.030 4788 Dihedral : 6.352 59.149 3944 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 14.33 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.15), residues: 3504 helix: 2.53 (0.11), residues: 2408 sheet: -0.84 (0.35), residues: 192 loop : -1.18 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.002 0.000 HIS B 259 PHE 0.022 0.001 PHE C 731 TYR 0.015 0.001 TYR C 999 ARG 0.002 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 287 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 885 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8378 (tmm-80) REVERT: A 1078 MET cc_start: 0.6292 (ptt) cc_final: 0.6023 (ptp) REVERT: B 750 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 793 TYR cc_start: 0.8296 (t80) cc_final: 0.8036 (t80) REVERT: B 866 ASP cc_start: 0.8902 (t0) cc_final: 0.8419 (t0) REVERT: B 885 ARG cc_start: 0.8788 (mtm180) cc_final: 0.8380 (tmm-80) REVERT: B 1020 TYR cc_start: 0.8648 (m-80) cc_final: 0.8184 (m-80) REVERT: C 750 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9155 (mp) REVERT: C 793 TYR cc_start: 0.8230 (t80) cc_final: 0.7902 (t80) REVERT: C 866 ASP cc_start: 0.8905 (t0) cc_final: 0.8410 (t0) REVERT: D 866 ASP cc_start: 0.8915 (t0) cc_final: 0.8551 (t0) REVERT: D 885 ARG cc_start: 0.8736 (mtm180) cc_final: 0.8450 (tmm-80) REVERT: D 973 ASN cc_start: 0.8805 (m110) cc_final: 0.8571 (m110) outliers start: 22 outliers final: 19 residues processed: 298 average time/residue: 0.6936 time to fit residues: 335.2439 Evaluate side-chains 298 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28596 Z= 0.305 Angle : 0.531 12.248 38896 Z= 0.283 Chirality : 0.036 0.153 4524 Planarity : 0.003 0.029 4788 Dihedral : 6.352 58.818 3944 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.94 % Allowed : 14.51 % Favored : 84.54 % 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: 1.83 (0.14), residues: 3504 helix: 2.24 (0.10), residues: 2428 sheet: -0.93 (0.35), residues: 192 loop : -1.24 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.005 0.001 HIS B 559 PHE 0.022 0.001 PHE C 731 TYR 0.011 0.001 TYR D 836 ARG 0.003 0.000 ARG D1008 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 TYR 186 is missing expected H atoms. Skipping. Residue MET 189 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue VAL 348 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 899 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue LEU 909 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 3.272 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: A 793 TYR cc_start: 0.8183 (t80) cc_final: 0.7928 (t80) REVERT: A 885 ARG cc_start: 0.8793 (mtm180) cc_final: 0.8404 (tmm-80) REVERT: A 1078 MET cc_start: 0.6334 (ptt) cc_final: 0.6054 (ptp) REVERT: B 750 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 793 TYR cc_start: 0.8340 (t80) cc_final: 0.8120 (t80) REVERT: B 866 ASP cc_start: 0.8882 (t0) cc_final: 0.8490 (t0) REVERT: B 885 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8452 (ttp-170) REVERT: B 1020 TYR cc_start: 0.8647 (m-80) cc_final: 0.8216 (m-80) REVERT: C 750 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9133 (mp) REVERT: C 866 ASP cc_start: 0.8883 (t0) cc_final: 0.8482 (t0) REVERT: D 866 ASP cc_start: 0.8899 (t0) cc_final: 0.8575 (t0) REVERT: D 885 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8458 (tmm-80) REVERT: D 973 ASN cc_start: 0.8858 (m110) cc_final: 0.8632 (m110) outliers start: 26 outliers final: 20 residues processed: 287 average time/residue: 0.7003 time to fit residues: 324.4468 Evaluate side-chains 285 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 263 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 757 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain D residue 240 TYR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.0060 chunk 300 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 260 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN C 676 ASN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088203 restraints weight = 201264.990| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.45 r_work: 0.3205 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 28596 Z= 0.145 Angle : 0.481 11.114 38896 Z= 0.250 Chirality : 0.035 0.149 4524 Planarity : 0.003 0.029 4788 Dihedral : 6.113 59.598 3944 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.94 % Allowed : 14.70 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.14), residues: 3504 helix: 2.49 (0.11), residues: 2432 sheet: -0.80 (0.35), residues: 192 loop : -1.11 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 426 HIS 0.002 0.000 HIS C 259 PHE 0.022 0.001 PHE C 731 TYR 0.014 0.001 TYR B 999 ARG 0.001 0.000 ARG D 890 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8732.73 seconds wall clock time: 151 minutes 49.23 seconds (9109.23 seconds total)