Starting phenix.real_space_refine on Sun Jun 22 17:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.map" model { file = "/net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x50_38057/06_2025/8x50_38057.cif" } resolution = 3.82 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= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16467 2.51 5 N 4200 2.21 5 O 5047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25828 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.69, per 1000 atoms: 0.61 Number of scatterers: 25828 At special positions: 0 Unit cell: (146.64, 135.2, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5047 8.00 N 4200 7.00 C 16467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 354 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 331 " " NAG D 1 " - " ASN A 354 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN C 354 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1098 " Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 3.4 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 52 sheets defined 25.9% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.521A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.925A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.687A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.832A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.737A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.587A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.682A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.995A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.506A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.424A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.535A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.100A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.251A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.505A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.909A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.694A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.431A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.276A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.883A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.549A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.854A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.562A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.936A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.812A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 618 through 627 removed outlier: 3.853A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.502A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.339A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.602A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.514A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.639A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.957A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.293A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.882A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.954A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.963A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.429A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.859A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 removed outlier: 7.969A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.899A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.926A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.669A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.439A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.915A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.758A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.088A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.021A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.027A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.090A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.804A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.158A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.373A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.124A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.690A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.040A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.046A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.603A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.226A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.289A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.286A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.668A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.567A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.699A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.013A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.948A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.687A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 6.842A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.563A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1077 through 1078 removed outlier: 3.791A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.556A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2499 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: 11.87 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8139 1.34 - 1.47: 6705 1.47 - 1.59: 11443 1.59 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 26428 Sorted by residual: bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.365 0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 4.10e+00 ... (remaining 26423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 35668 3.47 - 6.95: 282 6.95 - 10.42: 15 10.42 - 13.89: 2 13.89 - 17.37: 3 Bond angle restraints: 35970 Sorted by residual: angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 122.44 115.27 7.17 1.19e+00 7.06e-01 3.63e+01 angle pdb=" CB MET C 731 " pdb=" CG MET C 731 " pdb=" SD MET C 731 " ideal model delta sigma weight residual 112.70 130.07 -17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" N ILE C 210 " pdb=" CA ILE C 210 " pdb=" C ILE C 210 " ideal model delta sigma weight residual 106.32 115.01 -8.69 1.61e+00 3.86e-01 2.92e+01 angle pdb=" CB LYS B1038 " pdb=" CG LYS B1038 " pdb=" CD LYS B1038 " ideal model delta sigma weight residual 111.30 122.20 -10.90 2.30e+00 1.89e-01 2.25e+01 angle pdb=" CA LEU B 303 " pdb=" CB LEU B 303 " pdb=" CG LEU B 303 " ideal model delta sigma weight residual 116.30 132.58 -16.28 3.50e+00 8.16e-02 2.16e+01 ... (remaining 35965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 14732 23.13 - 46.26: 1377 46.26 - 69.40: 171 69.40 - 92.53: 148 92.53 - 115.66: 119 Dihedral angle restraints: 16547 sinusoidal: 7262 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -1.58 -84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 150.34 -57.34 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 148.49 31.51 0 5.00e+00 4.00e-02 3.97e+01 ... (remaining 16544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 4221 0.179 - 0.358: 30 0.358 - 0.537: 0 0.537 - 0.715: 0 0.715 - 0.894: 3 Chirality restraints: 4254 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 ... (remaining 4251 not shown) Planarity restraints: 4607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C1140 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 168 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C PHE C 168 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE C 168 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU C 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 896 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 897 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 897 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 897 " -0.034 5.00e-02 4.00e+02 ... (remaining 4604 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 561 2.65 - 3.21: 25209 3.21 - 3.77: 40918 3.77 - 4.34: 54297 4.34 - 4.90: 87055 Nonbonded interactions: 208040 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.087 3.040 nonbonded pdb=" O ARG C 319 " pdb=" OG1 THR C 630 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.122 3.040 nonbonded pdb=" O PHE B1075 " pdb=" OG1 THR B1076 " model vdw 2.148 3.040 nonbonded pdb=" O PHE C1075 " pdb=" OG1 THR C1076 " model vdw 2.151 3.040 ... (remaining 208035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 23 through 1144 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 62.400 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 0.045 26530 Z= 0.211 Angle : 0.846 18.130 36238 Z= 0.414 Chirality : 0.056 0.894 4254 Planarity : 0.005 0.109 4560 Dihedral : 21.375 115.660 10469 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 0.32 % Allowed : 26.57 % Favored : 73.11 % 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: -1.40 (0.15), residues: 3162 helix: 1.32 (0.21), residues: 676 sheet: -1.00 (0.20), residues: 638 loop : -1.85 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 353 HIS 0.005 0.001 HIS B 954 PHE 0.021 0.001 PHE C 592 TYR 0.033 0.002 TYR B 204 ARG 0.011 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 47) link_NAG-ASN : angle 4.00030 ( 141) link_BETA1-4 : bond 0.00429 ( 17) link_BETA1-4 : angle 2.18631 ( 51) hydrogen bonds : bond 0.21063 ( 905) hydrogen bonds : angle 8.58716 ( 2499) SS BOND : bond 0.00347 ( 38) SS BOND : angle 1.22293 ( 76) covalent geometry : bond 0.00437 (26428) covalent geometry : angle 0.80521 (35970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 2.757 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: A 55 PHE cc_start: 0.8505 (m-10) cc_final: 0.8266 (m-10) REVERT: A 191 GLU cc_start: 0.8299 (tp30) cc_final: 0.7922 (mm-30) REVERT: A 543 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: A 731 MET cc_start: 0.8483 (ptt) cc_final: 0.8240 (ptt) REVERT: A 1002 GLN cc_start: 0.9036 (tt0) cc_final: 0.8830 (tm-30) REVERT: B 106 PHE cc_start: 0.7772 (m-80) cc_final: 0.7547 (m-80) REVERT: B 740 MET cc_start: 0.8950 (tpp) cc_final: 0.8623 (tpp) REVERT: B 1050 MET cc_start: 0.8182 (mpp) cc_final: 0.7869 (mpp) outliers start: 9 outliers final: 5 residues processed: 183 average time/residue: 0.3217 time to fit residues: 99.4394 Evaluate side-chains 172 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 0.2980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 414 GLN A 417 ASN A 505 HIS A 690 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 544 ASN B 628 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.068623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050062 restraints weight = 131829.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051697 restraints weight = 73726.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052806 restraints weight = 50189.423| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26530 Z= 0.200 Angle : 0.806 15.911 36238 Z= 0.384 Chirality : 0.053 0.670 4254 Planarity : 0.005 0.072 4560 Dihedral : 12.535 115.670 4765 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.87 % Rotamer: Outliers : 4.93 % Allowed : 22.50 % Favored : 72.57 % 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: -1.31 (0.15), residues: 3162 helix: 1.43 (0.21), residues: 692 sheet: -0.74 (0.21), residues: 623 loop : -1.92 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.004 0.001 HIS B 954 PHE 0.023 0.002 PHE B 127 TYR 0.029 0.002 TYR A1067 ARG 0.012 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 47) link_NAG-ASN : angle 3.89195 ( 141) link_BETA1-4 : bond 0.00413 ( 17) link_BETA1-4 : angle 3.70460 ( 51) hydrogen bonds : bond 0.04465 ( 905) hydrogen bonds : angle 6.19500 ( 2499) SS BOND : bond 0.00343 ( 38) SS BOND : angle 1.26820 ( 76) covalent geometry : bond 0.00444 (26428) covalent geometry : angle 0.75687 (35970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 180 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.9204 (m-10) cc_final: 0.8892 (m-10) REVERT: A 543 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: A 664 ILE cc_start: 0.9618 (mt) cc_final: 0.9410 (mp) REVERT: A 759 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8311 (t80) REVERT: A 858 LEU cc_start: 0.9284 (tp) cc_final: 0.9064 (tp) REVERT: A 1029 MET cc_start: 0.8873 (tmm) cc_final: 0.8583 (tmm) REVERT: B 276 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9081 (mm) REVERT: B 629 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8008 (tp) REVERT: C 83 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 559 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6487 (m-10) REVERT: C 633 TRP cc_start: 0.8406 (p90) cc_final: 0.7953 (p90) REVERT: C 731 MET cc_start: 0.8716 (ppp) cc_final: 0.8440 (ppp) outliers start: 137 outliers final: 54 residues processed: 293 average time/residue: 0.3201 time to fit residues: 159.5616 Evaluate side-chains 207 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 228 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 283 optimal weight: 0.0020 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.068460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050014 restraints weight = 131093.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051638 restraints weight = 73700.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052723 restraints weight = 50233.330| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26530 Z= 0.149 Angle : 0.728 15.944 36238 Z= 0.347 Chirality : 0.050 0.599 4254 Planarity : 0.004 0.057 4560 Dihedral : 9.144 108.865 4758 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 3.74 % Allowed : 23.54 % Favored : 72.71 % 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: -1.28 (0.15), residues: 3162 helix: 1.48 (0.20), residues: 702 sheet: -0.92 (0.20), residues: 631 loop : -1.85 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 PHE 0.011 0.001 PHE C 338 TYR 0.023 0.001 TYR C 380 ARG 0.009 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 47) link_NAG-ASN : angle 3.84061 ( 141) link_BETA1-4 : bond 0.00449 ( 17) link_BETA1-4 : angle 3.19994 ( 51) hydrogen bonds : bond 0.04368 ( 905) hydrogen bonds : angle 5.82241 ( 2499) SS BOND : bond 0.00342 ( 38) SS BOND : angle 1.23607 ( 76) covalent geometry : bond 0.00327 (26428) covalent geometry : angle 0.67653 (35970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 165 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 175 PHE cc_start: 0.9173 (m-10) cc_final: 0.8794 (m-10) REVERT: A 191 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 543 PHE cc_start: 0.8303 (m-80) cc_final: 0.7932 (t80) REVERT: A 628 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: A 664 ILE cc_start: 0.9539 (mt) cc_final: 0.9324 (mp) REVERT: A 759 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8440 (t80) REVERT: A 858 LEU cc_start: 0.9223 (tp) cc_final: 0.8981 (tp) REVERT: A 1029 MET cc_start: 0.8913 (tmm) cc_final: 0.8521 (tmm) REVERT: B 119 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7261 (tp) REVERT: B 133 PHE cc_start: 0.7601 (p90) cc_final: 0.6942 (p90) REVERT: B 276 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9124 (mm) REVERT: B 374 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: B 461 LEU cc_start: 0.2868 (OUTLIER) cc_final: 0.2108 (tp) REVERT: B 725 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 856 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8789 (p0) REVERT: B 1029 MET cc_start: 0.9125 (tpp) cc_final: 0.8909 (tmm) REVERT: C 170 TYR cc_start: 0.7633 (t80) cc_final: 0.7305 (t80) REVERT: C 374 PHE cc_start: 0.6814 (m-10) cc_final: 0.6585 (m-10) REVERT: C 377 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6677 (t80) REVERT: C 400 PHE cc_start: 0.8755 (p90) cc_final: 0.8336 (p90) REVERT: C 497 PHE cc_start: 0.5408 (OUTLIER) cc_final: 0.4486 (m-80) REVERT: C 559 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: C 633 TRP cc_start: 0.8480 (p90) cc_final: 0.7950 (p90) REVERT: C 731 MET cc_start: 0.8702 (ppp) cc_final: 0.8033 (ppp) REVERT: C 740 MET cc_start: 0.8946 (tpp) cc_final: 0.8368 (tpp) REVERT: C 869 MET cc_start: 0.9281 (pmm) cc_final: 0.9042 (pmm) outliers start: 104 outliers final: 45 residues processed: 256 average time/residue: 0.3360 time to fit residues: 146.5135 Evaluate side-chains 200 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 265 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 224 optimal weight: 0.3980 chunk 212 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.066866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048705 restraints weight = 133230.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050281 restraints weight = 75106.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051344 restraints weight = 51316.113| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26530 Z= 0.193 Angle : 0.725 14.951 36238 Z= 0.351 Chirality : 0.049 0.593 4254 Planarity : 0.004 0.049 4560 Dihedral : 8.161 103.804 4756 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.52 % Rotamer: Outliers : 4.50 % Allowed : 23.61 % Favored : 71.89 % 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: -1.29 (0.15), residues: 3162 helix: 1.51 (0.21), residues: 692 sheet: -0.96 (0.21), residues: 619 loop : -1.84 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.005 0.001 HIS A1064 PHE 0.020 0.001 PHE A 106 TYR 0.017 0.002 TYR A 265 ARG 0.013 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 47) link_NAG-ASN : angle 3.79021 ( 141) link_BETA1-4 : bond 0.00342 ( 17) link_BETA1-4 : angle 2.77870 ( 51) hydrogen bonds : bond 0.04204 ( 905) hydrogen bonds : angle 5.66018 ( 2499) SS BOND : bond 0.00455 ( 38) SS BOND : angle 1.45923 ( 76) covalent geometry : bond 0.00431 (26428) covalent geometry : angle 0.67643 (35970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 147 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 191 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7795 (tp30) REVERT: A 402 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8355 (tp) REVERT: A 461 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6910 (tt) REVERT: A 495 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.2978 (m-80) REVERT: A 543 PHE cc_start: 0.8428 (m-80) cc_final: 0.8027 (t80) REVERT: A 664 ILE cc_start: 0.9524 (mt) cc_final: 0.9316 (mp) REVERT: A 759 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8506 (t80) REVERT: A 773 GLU cc_start: 0.8830 (tt0) cc_final: 0.7982 (tm-30) REVERT: A 869 MET cc_start: 0.9447 (pmm) cc_final: 0.9087 (pmm) REVERT: A 900 MET cc_start: 0.9168 (pmm) cc_final: 0.8883 (pmm) REVERT: A 1002 GLN cc_start: 0.9166 (tt0) cc_final: 0.8862 (tm-30) REVERT: A 1029 MET cc_start: 0.8910 (tmm) cc_final: 0.8439 (tmm) REVERT: B 119 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 133 PHE cc_start: 0.7524 (p90) cc_final: 0.6950 (p90) REVERT: B 276 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9057 (mm) REVERT: B 374 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: B 434 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8113 (mt) REVERT: B 461 LEU cc_start: 0.2721 (OUTLIER) cc_final: 0.1959 (tp) REVERT: C 55 PHE cc_start: 0.8818 (m-10) cc_final: 0.8595 (m-10) REVERT: C 400 PHE cc_start: 0.8801 (p90) cc_final: 0.8447 (p90) REVERT: C 559 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: C 633 TRP cc_start: 0.8589 (p90) cc_final: 0.8190 (p90) REVERT: C 731 MET cc_start: 0.8740 (ppp) cc_final: 0.8120 (ppp) REVERT: C 740 MET cc_start: 0.8992 (tpp) cc_final: 0.8668 (tpp) outliers start: 125 outliers final: 69 residues processed: 259 average time/residue: 0.3124 time to fit residues: 138.8947 Evaluate side-chains 213 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 133 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 157 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 125 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047651 restraints weight = 135901.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049236 restraints weight = 76106.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050264 restraints weight = 52080.660| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26530 Z= 0.168 Angle : 0.710 14.903 36238 Z= 0.343 Chirality : 0.049 0.594 4254 Planarity : 0.004 0.050 4560 Dihedral : 7.765 101.372 4756 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 4.64 % Allowed : 23.36 % Favored : 71.99 % 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: -1.22 (0.15), residues: 3162 helix: 1.62 (0.21), residues: 692 sheet: -0.92 (0.20), residues: 617 loop : -1.82 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS A 339 PHE 0.025 0.001 PHE C 377 TYR 0.027 0.001 TYR B 495 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 47) link_NAG-ASN : angle 3.75971 ( 141) link_BETA1-4 : bond 0.00356 ( 17) link_BETA1-4 : angle 2.27834 ( 51) hydrogen bonds : bond 0.04127 ( 905) hydrogen bonds : angle 5.53226 ( 2499) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.27788 ( 76) covalent geometry : bond 0.00377 (26428) covalent geometry : angle 0.66455 (35970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 149 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8897 (tp) REVERT: A 55 PHE cc_start: 0.8675 (m-10) cc_final: 0.8408 (m-10) REVERT: A 175 PHE cc_start: 0.9325 (m-10) cc_final: 0.9000 (m-10) REVERT: A 191 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7804 (tp30) REVERT: A 402 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8504 (tp) REVERT: A 461 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6921 (tt) REVERT: A 495 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.2932 (m-80) REVERT: A 543 PHE cc_start: 0.8480 (m-80) cc_final: 0.8062 (t80) REVERT: A 740 MET cc_start: 0.9216 (tmm) cc_final: 0.8833 (ppp) REVERT: A 773 GLU cc_start: 0.8852 (tt0) cc_final: 0.8158 (tm-30) REVERT: A 1002 GLN cc_start: 0.9159 (tt0) cc_final: 0.8869 (tm-30) REVERT: A 1029 MET cc_start: 0.8908 (tmm) cc_final: 0.8379 (tmm) REVERT: A 1039 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8575 (ptm160) REVERT: B 119 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 127 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: B 133 PHE cc_start: 0.7643 (p90) cc_final: 0.7353 (p90) REVERT: B 276 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9079 (mm) REVERT: B 461 LEU cc_start: 0.3231 (OUTLIER) cc_final: 0.2250 (tp) REVERT: B 611 LEU cc_start: 0.9546 (tp) cc_final: 0.9026 (tt) REVERT: C 55 PHE cc_start: 0.8847 (m-10) cc_final: 0.8596 (m-10) REVERT: C 170 TYR cc_start: 0.7646 (t80) cc_final: 0.7287 (t80) REVERT: C 319 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: C 400 PHE cc_start: 0.8865 (p90) cc_final: 0.8460 (p90) REVERT: C 497 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4605 (m-80) REVERT: C 559 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: C 633 TRP cc_start: 0.8660 (p90) cc_final: 0.8191 (p90) REVERT: C 731 MET cc_start: 0.8939 (ppp) cc_final: 0.8265 (ppp) REVERT: C 740 MET cc_start: 0.8958 (tpp) cc_final: 0.8486 (tpp) REVERT: C 1029 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8686 (tpp) outliers start: 129 outliers final: 75 residues processed: 262 average time/residue: 0.3163 time to fit residues: 139.9791 Evaluate side-chains 217 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 129 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 235 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 242 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 119 optimal weight: 0.0470 chunk 301 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.065738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047514 restraints weight = 134543.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049100 restraints weight = 75288.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050144 restraints weight = 51298.797| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26530 Z= 0.153 Angle : 0.692 14.794 36238 Z= 0.333 Chirality : 0.048 0.590 4254 Planarity : 0.004 0.060 4560 Dihedral : 7.589 101.553 4756 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.97 % Favored : 91.94 % Rotamer: Outliers : 4.39 % Allowed : 24.48 % Favored : 71.13 % 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: -1.20 (0.15), residues: 3162 helix: 1.62 (0.21), residues: 694 sheet: -0.91 (0.20), residues: 627 loop : -1.80 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.006 0.001 HIS A 339 PHE 0.024 0.001 PHE A 106 TYR 0.027 0.001 TYR B 265 ARG 0.008 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 47) link_NAG-ASN : angle 3.72491 ( 141) link_BETA1-4 : bond 0.00366 ( 17) link_BETA1-4 : angle 2.19325 ( 51) hydrogen bonds : bond 0.04000 ( 905) hydrogen bonds : angle 5.36957 ( 2499) SS BOND : bond 0.00449 ( 38) SS BOND : angle 1.28974 ( 76) covalent geometry : bond 0.00344 (26428) covalent geometry : angle 0.64584 (35970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 153 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8762 (tp) REVERT: A 53 ASP cc_start: 0.8861 (p0) cc_final: 0.8522 (p0) REVERT: A 55 PHE cc_start: 0.8696 (m-10) cc_final: 0.8296 (m-80) REVERT: A 175 PHE cc_start: 0.9316 (m-10) cc_final: 0.9013 (m-10) REVERT: A 191 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 402 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8560 (tp) REVERT: A 461 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6878 (tt) REVERT: A 495 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.3065 (m-80) REVERT: A 629 LEU cc_start: 0.8787 (tp) cc_final: 0.8572 (tt) REVERT: A 773 GLU cc_start: 0.8837 (tt0) cc_final: 0.8173 (tm-30) REVERT: A 1002 GLN cc_start: 0.9189 (tt0) cc_final: 0.8857 (tm-30) REVERT: A 1029 MET cc_start: 0.8890 (tmm) cc_final: 0.8322 (tmm) REVERT: A 1039 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8613 (ptm160) REVERT: B 127 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: B 133 PHE cc_start: 0.7649 (p90) cc_final: 0.7421 (p90) REVERT: B 461 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2213 (tp) REVERT: B 900 MET cc_start: 0.8985 (mmp) cc_final: 0.8651 (mmt) REVERT: C 127 PHE cc_start: 0.9018 (t80) cc_final: 0.8501 (t80) REVERT: C 170 TYR cc_start: 0.7742 (t80) cc_final: 0.7388 (t80) REVERT: C 319 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8358 (ttp80) REVERT: C 400 PHE cc_start: 0.8879 (p90) cc_final: 0.8477 (p90) REVERT: C 559 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: C 633 TRP cc_start: 0.8695 (p90) cc_final: 0.8162 (p90) REVERT: C 731 MET cc_start: 0.8941 (ppp) cc_final: 0.8283 (ppp) REVERT: C 740 MET cc_start: 0.8958 (tpp) cc_final: 0.8506 (tpp) outliers start: 122 outliers final: 78 residues processed: 260 average time/residue: 0.3210 time to fit residues: 146.1253 Evaluate side-chains 219 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 132 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 437 ASN B 487 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045189 restraints weight = 137566.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046686 restraints weight = 77470.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047691 restraints weight = 53010.934| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26530 Z= 0.249 Angle : 0.767 14.761 36238 Z= 0.378 Chirality : 0.049 0.582 4254 Planarity : 0.005 0.060 4560 Dihedral : 7.964 105.908 4756 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.04 % Favored : 90.89 % Rotamer: Outliers : 4.61 % Allowed : 24.98 % Favored : 70.41 % 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: -1.33 (0.15), residues: 3162 helix: 1.52 (0.21), residues: 685 sheet: -0.94 (0.20), residues: 641 loop : -1.90 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 633 HIS 0.006 0.001 HIS A 339 PHE 0.028 0.002 PHE C 374 TYR 0.019 0.002 TYR B 495 ARG 0.007 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 47) link_NAG-ASN : angle 3.72324 ( 141) link_BETA1-4 : bond 0.00353 ( 17) link_BETA1-4 : angle 2.18958 ( 51) hydrogen bonds : bond 0.04476 ( 905) hydrogen bonds : angle 5.57148 ( 2499) SS BOND : bond 0.00544 ( 38) SS BOND : angle 1.49458 ( 76) covalent geometry : bond 0.00547 (26428) covalent geometry : angle 0.72576 (35970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 126 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 53 ASP cc_start: 0.9059 (p0) cc_final: 0.8683 (p0) REVERT: A 55 PHE cc_start: 0.8718 (m-10) cc_final: 0.8325 (m-80) REVERT: A 175 PHE cc_start: 0.9318 (m-10) cc_final: 0.9031 (m-10) REVERT: A 191 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 402 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 546 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7380 (mm) REVERT: A 773 GLU cc_start: 0.8840 (tt0) cc_final: 0.8298 (tm-30) REVERT: A 1002 GLN cc_start: 0.9245 (tt0) cc_final: 0.8965 (tm-30) REVERT: A 1029 MET cc_start: 0.8918 (tmm) cc_final: 0.8375 (tmm) REVERT: A 1039 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8799 (ptm160) REVERT: B 117 LEU cc_start: 0.8860 (tp) cc_final: 0.8548 (tp) REVERT: B 127 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: B 276 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 374 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: B 461 LEU cc_start: 0.3223 (OUTLIER) cc_final: 0.2192 (tp) REVERT: B 487 ASN cc_start: 0.2072 (OUTLIER) cc_final: 0.1844 (p0) REVERT: B 904 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: B 1129 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8952 (t) REVERT: C 127 PHE cc_start: 0.8936 (t80) cc_final: 0.8406 (t80) REVERT: C 168 PHE cc_start: 0.8596 (t80) cc_final: 0.8149 (t80) REVERT: C 319 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8448 (ttp80) REVERT: C 400 PHE cc_start: 0.8930 (p90) cc_final: 0.8338 (p90) REVERT: C 497 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.4866 (m-80) REVERT: C 633 TRP cc_start: 0.8836 (p90) cc_final: 0.8510 (p90) REVERT: C 731 MET cc_start: 0.8979 (ppp) cc_final: 0.8254 (ppp) REVERT: C 740 MET cc_start: 0.9010 (tpp) cc_final: 0.8637 (tpp) REVERT: C 770 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9212 (tt) REVERT: C 1002 GLN cc_start: 0.8833 (tp40) cc_final: 0.8534 (tp40) REVERT: C 1029 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8731 (tpp) outliers start: 128 outliers final: 88 residues processed: 242 average time/residue: 0.3215 time to fit residues: 132.7936 Evaluate side-chains 220 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 117 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 233 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046233 restraints weight = 135096.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047776 restraints weight = 75605.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048807 restraints weight = 51645.704| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26530 Z= 0.146 Angle : 0.704 14.611 36238 Z= 0.340 Chirality : 0.049 0.596 4254 Planarity : 0.004 0.053 4560 Dihedral : 7.705 104.356 4756 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 3.82 % Allowed : 25.95 % Favored : 70.23 % 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: -1.20 (0.15), residues: 3162 helix: 1.69 (0.21), residues: 685 sheet: -0.80 (0.21), residues: 630 loop : -1.86 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 633 HIS 0.006 0.001 HIS A 339 PHE 0.022 0.001 PHE B 375 TYR 0.022 0.001 TYR A 265 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 47) link_NAG-ASN : angle 3.69347 ( 141) link_BETA1-4 : bond 0.00388 ( 17) link_BETA1-4 : angle 2.10575 ( 51) hydrogen bonds : bond 0.04127 ( 905) hydrogen bonds : angle 5.35257 ( 2499) SS BOND : bond 0.00401 ( 38) SS BOND : angle 1.42135 ( 76) covalent geometry : bond 0.00330 (26428) covalent geometry : angle 0.65931 (35970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 138 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 53 ASP cc_start: 0.9026 (p0) cc_final: 0.8532 (p0) REVERT: A 55 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: A 175 PHE cc_start: 0.9275 (m-10) cc_final: 0.9010 (m-10) REVERT: A 191 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 342 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8524 (m-10) REVERT: A 402 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 629 LEU cc_start: 0.8923 (tp) cc_final: 0.8655 (tt) REVERT: A 740 MET cc_start: 0.9250 (tmm) cc_final: 0.9039 (ppp) REVERT: A 773 GLU cc_start: 0.8853 (tt0) cc_final: 0.8273 (tm-30) REVERT: A 869 MET cc_start: 0.9288 (pmm) cc_final: 0.9067 (pmm) REVERT: A 1002 GLN cc_start: 0.9251 (tt0) cc_final: 0.8915 (tm-30) REVERT: A 1029 MET cc_start: 0.8902 (tmm) cc_final: 0.8345 (tmm) REVERT: A 1039 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8690 (ptm160) REVERT: B 55 PHE cc_start: 0.8462 (m-10) cc_final: 0.8230 (m-10) REVERT: B 127 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: B 200 TYR cc_start: 0.7911 (m-80) cc_final: 0.7647 (m-80) REVERT: B 276 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8940 (mm) REVERT: B 346 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5963 (tpt90) REVERT: B 374 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: B 461 LEU cc_start: 0.2997 (OUTLIER) cc_final: 0.1705 (tp) REVERT: B 1111 GLU cc_start: 0.9065 (tp30) cc_final: 0.8598 (tm-30) REVERT: B 1129 VAL cc_start: 0.9221 (t) cc_final: 0.8984 (t) REVERT: C 92 PHE cc_start: 0.8883 (t80) cc_final: 0.8474 (t80) REVERT: C 127 PHE cc_start: 0.8956 (t80) cc_final: 0.8434 (t80) REVERT: C 170 TYR cc_start: 0.7730 (t80) cc_final: 0.7365 (t80) REVERT: C 400 PHE cc_start: 0.8956 (p90) cc_final: 0.8560 (p90) REVERT: C 490 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (m-10) REVERT: C 633 TRP cc_start: 0.8840 (p90) cc_final: 0.8217 (p90) REVERT: C 731 MET cc_start: 0.8953 (ppp) cc_final: 0.8246 (ppp) REVERT: C 740 MET cc_start: 0.8989 (tpp) cc_final: 0.8570 (tpp) outliers start: 106 outliers final: 79 residues processed: 232 average time/residue: 0.3272 time to fit residues: 129.9833 Evaluate side-chains 216 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 126 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 173 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.062997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.045132 restraints weight = 137119.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046660 restraints weight = 76883.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047659 restraints weight = 52510.479| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26530 Z= 0.198 Angle : 0.735 15.776 36238 Z= 0.356 Chirality : 0.049 0.595 4254 Planarity : 0.004 0.052 4560 Dihedral : 7.796 105.334 4756 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 3.64 % Allowed : 26.31 % Favored : 70.05 % 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: -1.25 (0.15), residues: 3162 helix: 1.59 (0.20), residues: 691 sheet: -0.82 (0.21), residues: 646 loop : -1.90 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.007 0.001 HIS A 339 PHE 0.018 0.002 PHE B 127 TYR 0.021 0.002 TYR B 917 ARG 0.005 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 47) link_NAG-ASN : angle 3.68706 ( 141) link_BETA1-4 : bond 0.00335 ( 17) link_BETA1-4 : angle 2.10908 ( 51) hydrogen bonds : bond 0.04251 ( 905) hydrogen bonds : angle 5.41878 ( 2499) SS BOND : bond 0.00428 ( 38) SS BOND : angle 1.36911 ( 76) covalent geometry : bond 0.00441 (26428) covalent geometry : angle 0.69328 (35970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 125 time to evaluate : 2.891 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: A 50 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8688 (tp) REVERT: A 53 ASP cc_start: 0.9014 (p0) cc_final: 0.8391 (p0) REVERT: A 55 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: A 175 PHE cc_start: 0.9265 (m-10) cc_final: 0.8948 (m-10) REVERT: A 191 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 402 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 495 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.3414 (m-80) REVERT: A 773 GLU cc_start: 0.8811 (tt0) cc_final: 0.8278 (tm-30) REVERT: A 869 MET cc_start: 0.9290 (pmm) cc_final: 0.9055 (pmm) REVERT: A 1002 GLN cc_start: 0.9246 (tt0) cc_final: 0.8955 (tm-30) REVERT: A 1029 MET cc_start: 0.8908 (tmm) cc_final: 0.8347 (tmm) REVERT: B 127 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: B 276 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8888 (mm) REVERT: B 374 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: B 461 LEU cc_start: 0.2980 (OUTLIER) cc_final: 0.1678 (tp) REVERT: B 1029 MET cc_start: 0.9027 (tpp) cc_final: 0.8770 (tmm) REVERT: B 1111 GLU cc_start: 0.9075 (tp30) cc_final: 0.8625 (tm-30) REVERT: B 1129 VAL cc_start: 0.9241 (t) cc_final: 0.9013 (t) REVERT: C 92 PHE cc_start: 0.8889 (t80) cc_final: 0.8487 (t80) REVERT: C 127 PHE cc_start: 0.8915 (t80) cc_final: 0.8346 (t80) REVERT: C 226 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9064 (mm) REVERT: C 400 PHE cc_start: 0.9061 (p90) cc_final: 0.8659 (p90) REVERT: C 423 TYR cc_start: 0.7520 (t80) cc_final: 0.7276 (t80) REVERT: C 633 TRP cc_start: 0.8883 (p90) cc_final: 0.8417 (p90) REVERT: C 731 MET cc_start: 0.8902 (ppp) cc_final: 0.8212 (ppp) REVERT: C 740 MET cc_start: 0.8984 (tpp) cc_final: 0.8611 (tpp) REVERT: C 770 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9185 (tt) REVERT: C 1002 GLN cc_start: 0.8829 (tp40) cc_final: 0.8535 (tp40) outliers start: 101 outliers final: 78 residues processed: 215 average time/residue: 0.3313 time to fit residues: 121.5671 Evaluate side-chains 207 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 119 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 121 ASN B 437 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.064177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046333 restraints weight = 134478.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047870 restraints weight = 75711.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048890 restraints weight = 51752.347| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26530 Z= 0.126 Angle : 0.701 15.578 36238 Z= 0.334 Chirality : 0.049 0.607 4254 Planarity : 0.004 0.053 4560 Dihedral : 7.539 103.427 4756 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 3.31 % Allowed : 26.71 % Favored : 69.98 % 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: -1.15 (0.15), residues: 3162 helix: 1.68 (0.21), residues: 690 sheet: -0.75 (0.21), residues: 630 loop : -1.82 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 633 HIS 0.006 0.001 HIS A 339 PHE 0.017 0.001 PHE B 216 TYR 0.022 0.001 TYR A 265 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 47) link_NAG-ASN : angle 3.67099 ( 141) link_BETA1-4 : bond 0.00422 ( 17) link_BETA1-4 : angle 2.07152 ( 51) hydrogen bonds : bond 0.03974 ( 905) hydrogen bonds : angle 5.25214 ( 2499) SS BOND : bond 0.00390 ( 38) SS BOND : angle 1.18635 ( 76) covalent geometry : bond 0.00287 (26428) covalent geometry : angle 0.65809 (35970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 135 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 53 ASP cc_start: 0.9024 (p0) cc_final: 0.8219 (p0) REVERT: A 55 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: A 175 PHE cc_start: 0.9244 (m-10) cc_final: 0.8955 (m-10) REVERT: A 191 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 342 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8570 (m-10) REVERT: A 402 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8728 (tp) REVERT: A 495 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: A 773 GLU cc_start: 0.8864 (tt0) cc_final: 0.8244 (tm-30) REVERT: A 869 MET cc_start: 0.9254 (pmm) cc_final: 0.9043 (pmm) REVERT: A 1002 GLN cc_start: 0.9252 (tt0) cc_final: 0.8870 (tm-30) REVERT: A 1029 MET cc_start: 0.8914 (tmm) cc_final: 0.8337 (tmm) REVERT: A 1039 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8622 (ptm160) REVERT: B 127 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 374 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: B 461 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.1794 (tp) REVERT: B 1029 MET cc_start: 0.9037 (tpp) cc_final: 0.8765 (tmm) REVERT: B 1111 GLU cc_start: 0.9107 (tp30) cc_final: 0.8637 (tm-30) REVERT: B 1129 VAL cc_start: 0.9260 (t) cc_final: 0.9027 (t) REVERT: C 92 PHE cc_start: 0.8840 (t80) cc_final: 0.8451 (t80) REVERT: C 127 PHE cc_start: 0.8956 (t80) cc_final: 0.8375 (t80) REVERT: C 170 TYR cc_start: 0.7753 (t80) cc_final: 0.7388 (t80) REVERT: C 226 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9026 (mm) REVERT: C 400 PHE cc_start: 0.8996 (p90) cc_final: 0.8620 (p90) REVERT: C 423 TYR cc_start: 0.7521 (t80) cc_final: 0.7273 (t80) REVERT: C 633 TRP cc_start: 0.8921 (p90) cc_final: 0.8183 (p90) REVERT: C 731 MET cc_start: 0.8961 (ppp) cc_final: 0.8238 (ppp) REVERT: C 740 MET cc_start: 0.9023 (tpp) cc_final: 0.8557 (tpp) outliers start: 92 outliers final: 75 residues processed: 219 average time/residue: 0.3183 time to fit residues: 119.0770 Evaluate side-chains 211 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 126 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 118 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 268 optimal weight: 0.0670 chunk 244 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047648 restraints weight = 135424.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049208 restraints weight = 75887.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050240 restraints weight = 51729.838| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26530 Z= 0.114 Angle : 0.701 15.549 36238 Z= 0.332 Chirality : 0.049 0.607 4254 Planarity : 0.004 0.069 4560 Dihedral : 7.290 101.243 4756 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 2.81 % Allowed : 27.21 % Favored : 69.98 % 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: -1.09 (0.15), residues: 3162 helix: 1.70 (0.21), residues: 693 sheet: -0.68 (0.22), residues: 603 loop : -1.78 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 633 HIS 0.014 0.001 HIS B 207 PHE 0.024 0.001 PHE A 106 TYR 0.023 0.001 TYR A 265 ARG 0.015 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 47) link_NAG-ASN : angle 3.63081 ( 141) link_BETA1-4 : bond 0.00447 ( 17) link_BETA1-4 : angle 2.04425 ( 51) hydrogen bonds : bond 0.03801 ( 905) hydrogen bonds : angle 5.14494 ( 2499) SS BOND : bond 0.00338 ( 38) SS BOND : angle 1.10928 ( 76) covalent geometry : bond 0.00256 (26428) covalent geometry : angle 0.65957 (35970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8067.55 seconds wall clock time: 142 minutes 31.88 seconds (8551.88 seconds total)