Starting phenix.real_space_refine on Mon Aug 25 07:27:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x50_38057/08_2025/8x50_38057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x50_38057/08_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_38057/08_2025/8x50_38057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x50_38057/08_2025/8x50_38057.map" model { file = "/net/cci-nas-00/data/ceres_data/8x50_38057/08_2025/8x50_38057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x50_38057/08_2025/8x50_38057.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.95, per 1000 atoms: 0.23 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: 2.10 Conformation dependent library (CDL) restraints added in 756.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.17 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: 5.64 Time building geometry restraints manager: 2.83 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 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: 2.470 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.340 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG C 214 TYR 0.033 0.002 TYR B 204 PHE 0.021 0.001 PHE C 592 TRP 0.038 0.003 TRP C 353 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00437 (26428) covalent geometry : angle 0.80521 (35970) SS BOND : bond 0.00347 ( 38) SS BOND : angle 1.22293 ( 76) hydrogen bonds : bond 0.21063 ( 905) hydrogen bonds : angle 8.58716 ( 2499) link_BETA1-4 : bond 0.00429 ( 17) link_BETA1-4 : angle 2.18631 ( 51) link_NAG-ASN : bond 0.00567 ( 47) link_NAG-ASN : angle 4.00030 ( 141) *********************** 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 : 0.903 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: 0.8624 (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: 0.1370 time to fit residues: 43.0816 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 : 0.981 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN 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 = 0.3600 r_free = 0.3600 target = 0.069313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.050692 restraints weight = 132390.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052329 restraints weight = 74513.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053438 restraints weight = 50793.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054183 restraints weight = 38997.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054681 restraints weight = 32515.174| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26530 Z= 0.187 Angle : 0.786 15.581 36238 Z= 0.374 Chirality : 0.052 0.653 4254 Planarity : 0.005 0.073 4560 Dihedral : 13.656 113.281 4765 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.90 % Rotamer: Outliers : 4.46 % Allowed : 22.68 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3162 helix: 1.47 (0.21), residues: 692 sheet: -0.71 (0.21), residues: 621 loop : -1.88 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 273 TYR 0.028 0.002 TYR A1067 PHE 0.021 0.002 PHE B 55 TRP 0.015 0.002 TRP C 353 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00411 (26428) covalent geometry : angle 0.73663 (35970) SS BOND : bond 0.00325 ( 38) SS BOND : angle 1.25242 ( 76) hydrogen bonds : bond 0.04306 ( 905) hydrogen bonds : angle 6.25396 ( 2499) link_BETA1-4 : bond 0.00357 ( 17) link_BETA1-4 : angle 3.48145 ( 51) link_NAG-ASN : bond 0.00604 ( 47) link_NAG-ASN : angle 3.88586 ( 141) *********************** 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 308 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 184 time to evaluate : 0.934 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: 0.9187 (m-10) cc_final: 0.8957 (m-10) REVERT: A 543 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: A 664 ILE cc_start: 0.9618 (mt) cc_final: 0.9409 (mp) REVERT: A 759 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8275 (t80) REVERT: A 773 GLU cc_start: 0.8581 (mp0) cc_final: 0.8376 (mm-30) REVERT: A 858 LEU cc_start: 0.9290 (tp) cc_final: 0.9075 (tp) REVERT: A 1029 MET cc_start: 0.8900 (tmm) cc_final: 0.8612 (tmm) REVERT: B 129 LYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5734 (mtpt) REVERT: B 276 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 629 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7997 (tp) REVERT: C 633 TRP cc_start: 0.8381 (p90) cc_final: 0.7887 (p90) REVERT: C 731 MET cc_start: 0.8758 (ppp) cc_final: 0.8471 (ppp) outliers start: 124 outliers final: 47 residues processed: 284 average time/residue: 0.1360 time to fit residues: 65.8852 Evaluate side-chains 199 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 615 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 1136 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 159 VAL 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 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 129 LYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 15 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 267 optimal weight: 0.0770 chunk 88 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 225 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 253 optimal weight: 0.0970 chunk 262 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 2.0140 ------------------------------------------------------------------------------- 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 417 ASN A 628 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.069010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050540 restraints weight = 132289.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052191 restraints weight = 74377.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053297 restraints weight = 50568.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054046 restraints weight = 38732.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054543 restraints weight = 32274.838| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1788 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= 0.144 Angle : 0.730 15.049 36238 Z= 0.347 Chirality : 0.050 0.603 4254 Planarity : 0.004 0.059 4560 Dihedral : 9.873 109.550 4758 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.47 % Rotamer: Outliers : 3.92 % Allowed : 23.29 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 3162 helix: 1.44 (0.20), residues: 702 sheet: -0.81 (0.21), residues: 619 loop : -1.85 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.022 0.001 TYR C 380 PHE 0.011 0.001 PHE C 338 TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00319 (26428) covalent geometry : angle 0.67864 (35970) SS BOND : bond 0.00369 ( 38) SS BOND : angle 1.32462 ( 76) hydrogen bonds : bond 0.04331 ( 905) hydrogen bonds : angle 5.87025 ( 2499) link_BETA1-4 : bond 0.00431 ( 17) link_BETA1-4 : angle 3.22745 ( 51) link_NAG-ASN : bond 0.00561 ( 47) link_NAG-ASN : angle 3.82975 ( 141) *********************** 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 279 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 170 time to evaluate : 0.982 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: 0.9258 (OUTLIER) cc_final: 0.8928 (tp) REVERT: A 175 PHE cc_start: 0.9149 (m-10) cc_final: 0.8817 (m-10) REVERT: A 191 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 543 PHE cc_start: 0.8304 (m-80) cc_final: 0.7941 (t80) REVERT: A 664 ILE cc_start: 0.9540 (mt) cc_final: 0.9317 (mp) REVERT: A 759 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 773 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (mm-30) REVERT: A 858 LEU cc_start: 0.9247 (tp) cc_final: 0.9021 (tp) REVERT: A 1002 GLN cc_start: 0.9126 (tt0) cc_final: 0.8801 (tm-30) REVERT: A 1029 MET cc_start: 0.8927 (tmm) cc_final: 0.8552 (tmm) REVERT: B 133 PHE cc_start: 0.7578 (p90) cc_final: 0.6960 (p90) REVERT: B 276 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9099 (mm) REVERT: B 374 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: B 847 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8295 (mtm180) REVERT: B 856 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8686 (p0) REVERT: B 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.8912 (tmm) REVERT: C 170 TYR cc_start: 0.7603 (t80) cc_final: 0.7287 (t80) REVERT: C 374 PHE cc_start: 0.6836 (m-10) cc_final: 0.6544 (m-10) REVERT: C 377 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6563 (t80) REVERT: C 497 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: C 559 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: C 633 TRP cc_start: 0.8469 (p90) cc_final: 0.7980 (p90) REVERT: C 731 MET cc_start: 0.8762 (ppp) cc_final: 0.8038 (ppp) REVERT: C 740 MET cc_start: 0.8956 (tpp) cc_final: 0.8311 (tpt) REVERT: C 869 MET cc_start: 0.9277 (pmm) cc_final: 0.9029 (pmm) outliers start: 109 outliers final: 53 residues processed: 267 average time/residue: 0.1514 time to fit residues: 68.4021 Evaluate side-chains 212 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 511 VAL 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 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 773 GLU 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 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 455 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 723 THR 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 951 VAL 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 1141 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 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 546 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 595 VAL 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 1029 MET 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 229 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.066914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048753 restraints weight = 132987.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050326 restraints weight = 75093.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051379 restraints weight = 51454.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052113 restraints weight = 39685.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052609 restraints weight = 33105.762| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26530 Z= 0.205 Angle : 0.738 14.996 36238 Z= 0.357 Chirality : 0.049 0.588 4254 Planarity : 0.005 0.054 4560 Dihedral : 8.339 105.452 4756 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.82 % Favored : 91.08 % Rotamer: Outliers : 4.86 % Allowed : 23.36 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.15), residues: 3162 helix: 1.48 (0.20), residues: 698 sheet: -0.95 (0.21), residues: 618 loop : -1.88 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 346 TYR 0.021 0.002 TYR C 451 PHE 0.022 0.002 PHE C 490 TRP 0.008 0.001 TRP B1102 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00452 (26428) covalent geometry : angle 0.68896 (35970) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.55024 ( 76) hydrogen bonds : bond 0.04262 ( 905) hydrogen bonds : angle 5.72554 ( 2499) link_BETA1-4 : bond 0.00333 ( 17) link_BETA1-4 : angle 2.88994 ( 51) link_NAG-ASN : bond 0.00562 ( 47) link_NAG-ASN : angle 3.81053 ( 141) *********************** 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 284 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 149 time to evaluate : 0.772 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: 0.9232 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 191 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7783 (tp30) REVERT: A 402 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8365 (tp) REVERT: A 461 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6912 (tt) REVERT: A 495 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.2823 (m-80) REVERT: A 543 PHE cc_start: 0.8415 (m-80) cc_final: 0.7995 (t80) REVERT: A 664 ILE cc_start: 0.9510 (mt) cc_final: 0.9300 (mp) REVERT: A 759 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8540 (t80) REVERT: A 773 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: A 1029 MET cc_start: 0.8936 (tmm) cc_final: 0.8466 (tmm) REVERT: B 133 PHE cc_start: 0.7611 (p90) cc_final: 0.7248 (p90) REVERT: B 276 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9038 (mm) REVERT: B 374 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6681 (m-80) REVERT: B 434 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 461 LEU cc_start: 0.2548 (OUTLIER) cc_final: 0.1798 (tp) REVERT: B 856 ASN cc_start: 0.9268 (m-40) cc_final: 0.9065 (m-40) REVERT: C 374 PHE cc_start: 0.6776 (m-10) cc_final: 0.6317 (m-10) REVERT: C 400 PHE cc_start: 0.8772 (p90) cc_final: 0.8413 (p90) REVERT: C 633 TRP cc_start: 0.8586 (p90) cc_final: 0.8209 (p90) REVERT: C 731 MET cc_start: 0.8912 (ppp) cc_final: 0.8109 (ppp) REVERT: C 740 MET cc_start: 0.9007 (tpp) cc_final: 0.8635 (tpp) outliers start: 135 outliers final: 84 residues processed: 265 average time/residue: 0.1380 time to fit residues: 62.4999 Evaluate side-chains 225 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 131 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE 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 759 PHE Chi-restraints excluded: chain A residue 773 GLU 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 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 159 VAL 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 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 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 866 THR Chi-restraints excluded: chain B residue 936 ASP 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 979 ASP Chi-restraints excluded: chain B residue 1050 MET 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 B residue 1141 LEU Chi-restraints excluded: chain C residue 177 MET 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 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 430 THR 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 546 LEU 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 734 THR Chi-restraints excluded: chain C residue 747 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 143 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048631 restraints weight = 132336.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050222 restraints weight = 74404.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051288 restraints weight = 50780.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051994 restraints weight = 39144.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052482 restraints weight = 32828.064| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26530 Z= 0.150 Angle : 0.699 14.783 36238 Z= 0.337 Chirality : 0.049 0.598 4254 Planarity : 0.004 0.053 4560 Dihedral : 7.902 102.637 4756 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % Rotamer: Outliers : 4.57 % Allowed : 24.19 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3162 helix: 1.63 (0.21), residues: 698 sheet: -0.94 (0.20), residues: 623 loop : -1.84 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.029 0.001 TYR B 495 PHE 0.044 0.001 PHE C 374 TRP 0.007 0.001 TRP C1102 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00341 (26428) covalent geometry : angle 0.65076 (35970) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.43486 ( 76) hydrogen bonds : bond 0.04044 ( 905) hydrogen bonds : angle 5.56189 ( 2499) link_BETA1-4 : bond 0.00379 ( 17) link_BETA1-4 : angle 2.50328 ( 51) link_NAG-ASN : bond 0.00533 ( 47) link_NAG-ASN : angle 3.75118 ( 141) *********************** 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 272 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 145 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8933 (tp) REVERT: A 175 PHE cc_start: 0.9274 (m-10) cc_final: 0.8991 (m-10) REVERT: A 191 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7773 (tp30) REVERT: A 402 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 461 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6916 (tt) REVERT: A 495 TYR cc_start: 0.5483 (OUTLIER) cc_final: 0.2795 (m-80) REVERT: A 543 PHE cc_start: 0.8469 (m-80) cc_final: 0.8048 (t80) REVERT: A 664 ILE cc_start: 0.9485 (mt) cc_final: 0.9278 (mp) REVERT: A 759 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8518 (t80) REVERT: A 868 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8455 (tp30) REVERT: A 900 MET cc_start: 0.9078 (pmm) cc_final: 0.8872 (pmm) REVERT: A 1002 GLN cc_start: 0.9173 (tt0) cc_final: 0.8853 (tm-30) REVERT: A 1029 MET cc_start: 0.8928 (tmm) cc_final: 0.8416 (tmm) REVERT: A 1039 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8602 (ptm160) REVERT: B 119 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7260 (tp) REVERT: B 127 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: B 133 PHE cc_start: 0.7683 (p90) cc_final: 0.7375 (p90) REVERT: B 276 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9068 (mm) REVERT: B 374 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: B 434 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8124 (mt) REVERT: B 461 LEU cc_start: 0.2720 (OUTLIER) cc_final: 0.1927 (tp) REVERT: C 55 PHE cc_start: 0.8841 (m-10) cc_final: 0.8572 (m-10) REVERT: C 170 TYR cc_start: 0.7655 (t80) cc_final: 0.7301 (t80) REVERT: C 400 PHE cc_start: 0.8820 (p90) cc_final: 0.8452 (p90) REVERT: C 497 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: C 633 TRP cc_start: 0.8600 (p90) cc_final: 0.8082 (p90) REVERT: C 731 MET cc_start: 0.8881 (ppp) cc_final: 0.8058 (ppp) REVERT: C 740 MET cc_start: 0.8987 (tpp) cc_final: 0.8438 (tpp) REVERT: C 1029 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8748 (tpp) outliers start: 127 outliers final: 71 residues processed: 256 average time/residue: 0.1353 time to fit residues: 59.7382 Evaluate side-chains 216 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 338 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE 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 611 LEU 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 759 PHE 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 867 ASP 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 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 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 492 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 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 264 ASP Chi-restraints excluded: chain C residue 308 VAL 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 430 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 546 LEU 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 1029 MET Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 51 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047817 restraints weight = 132812.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049393 restraints weight = 74408.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050440 restraints weight = 50609.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051150 restraints weight = 39017.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051622 restraints weight = 32648.033| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26530 Z= 0.160 Angle : 0.702 14.686 36238 Z= 0.338 Chirality : 0.048 0.589 4254 Planarity : 0.004 0.053 4560 Dihedral : 7.614 102.532 4756 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.22 % Favored : 91.68 % Rotamer: Outliers : 4.68 % Allowed : 24.15 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.15), residues: 3162 helix: 1.68 (0.21), residues: 686 sheet: -0.96 (0.20), residues: 633 loop : -1.77 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.024 0.001 TYR B 265 PHE 0.015 0.001 PHE B 127 TRP 0.009 0.001 TRP C 104 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00360 (26428) covalent geometry : angle 0.65670 (35970) SS BOND : bond 0.00329 ( 38) SS BOND : angle 1.29080 ( 76) hydrogen bonds : bond 0.04039 ( 905) hydrogen bonds : angle 5.41609 ( 2499) link_BETA1-4 : bond 0.00360 ( 17) link_BETA1-4 : angle 2.22659 ( 51) link_NAG-ASN : bond 0.00530 ( 47) link_NAG-ASN : angle 3.71178 ( 141) *********************** 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 272 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 142 time to evaluate : 0.747 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: 0.9166 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 55 PHE cc_start: 0.8700 (m-10) cc_final: 0.8471 (m-10) REVERT: A 175 PHE cc_start: 0.9282 (m-10) cc_final: 0.9001 (m-10) REVERT: A 191 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7743 (tp30) REVERT: A 402 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 461 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6893 (tt) REVERT: A 495 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.2968 (m-80) REVERT: A 664 ILE cc_start: 0.9457 (mt) cc_final: 0.9227 (mp) REVERT: A 773 GLU cc_start: 0.8799 (tt0) cc_final: 0.8376 (tm-30) REVERT: A 1002 GLN cc_start: 0.9182 (tt0) cc_final: 0.8858 (tm-30) REVERT: A 1029 MET cc_start: 0.8900 (tmm) cc_final: 0.8343 (tmm) REVERT: A 1039 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8142 (ptm160) REVERT: B 127 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: B 374 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 434 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 461 LEU cc_start: 0.2787 (OUTLIER) cc_final: 0.1848 (tp) REVERT: B 489 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.5386 (m-80) REVERT: B 740 MET cc_start: 0.9133 (tpp) cc_final: 0.8846 (tpp) REVERT: B 900 MET cc_start: 0.8975 (mmp) cc_final: 0.8719 (mmt) REVERT: C 55 PHE cc_start: 0.8943 (m-10) cc_final: 0.8621 (m-10) REVERT: C 170 TYR cc_start: 0.7686 (t80) cc_final: 0.7305 (t80) REVERT: C 400 PHE cc_start: 0.8885 (p90) cc_final: 0.8496 (p90) REVERT: C 633 TRP cc_start: 0.8715 (p90) cc_final: 0.8198 (p90) REVERT: C 731 MET cc_start: 0.8967 (ppp) cc_final: 0.8148 (ppp) REVERT: C 740 MET cc_start: 0.8994 (tpp) cc_final: 0.8517 (tpp) REVERT: C 1029 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8717 (tpp) REVERT: C 1039 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7457 (mtm-85) outliers start: 130 outliers final: 85 residues processed: 257 average time/residue: 0.1383 time to fit residues: 61.0971 Evaluate side-chains 231 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 134 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 392 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 611 LEU 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 167 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 240 THR 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 487 ASN Chi-restraints excluded: chain B residue 489 TYR 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 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL 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 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 343 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR 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 546 LEU 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 734 THR 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 996 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 105 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** 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** C 321 GLN C 437 ASN C 907 ASN C1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045413 restraints weight = 136990.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046917 restraints weight = 77134.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.047926 restraints weight = 52898.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048592 restraints weight = 40964.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049061 restraints weight = 34553.365| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 26530 Z= 0.261 Angle : 0.775 15.616 36238 Z= 0.380 Chirality : 0.049 0.582 4254 Planarity : 0.005 0.056 4560 Dihedral : 7.978 106.066 4756 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.11 % Favored : 90.83 % Rotamer: Outliers : 4.72 % Allowed : 24.77 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.15), residues: 3162 helix: 1.43 (0.21), residues: 693 sheet: -0.92 (0.20), residues: 634 loop : -1.91 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.020 0.002 TYR B 453 PHE 0.023 0.002 PHE B 127 TRP 0.009 0.002 TRP A 633 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00571 (26428) covalent geometry : angle 0.73449 (35970) SS BOND : bond 0.00407 ( 38) SS BOND : angle 1.42885 ( 76) hydrogen bonds : bond 0.04446 ( 905) hydrogen bonds : angle 5.62063 ( 2499) link_BETA1-4 : bond 0.00365 ( 17) link_BETA1-4 : angle 2.19070 ( 51) link_NAG-ASN : bond 0.00592 ( 47) link_NAG-ASN : angle 3.74180 ( 141) *********************** 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 263 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 132 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8853 (tp) REVERT: A 53 ASP cc_start: 0.8927 (p0) cc_final: 0.8663 (p0) REVERT: A 55 PHE cc_start: 0.8685 (m-10) cc_final: 0.8322 (m-80) REVERT: A 175 PHE cc_start: 0.9262 (m-10) cc_final: 0.8935 (m-10) REVERT: A 191 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 402 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 664 ILE cc_start: 0.9510 (mt) cc_final: 0.9299 (mp) REVERT: A 740 MET cc_start: 0.9192 (tmm) cc_final: 0.8971 (ppp) REVERT: A 773 GLU cc_start: 0.8796 (tt0) cc_final: 0.8462 (tm-30) REVERT: A 1002 GLN cc_start: 0.9254 (tt0) cc_final: 0.8963 (tm-30) REVERT: A 1029 MET cc_start: 0.8889 (tmm) cc_final: 0.8378 (tmm) REVERT: B 127 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: B 276 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8973 (mm) REVERT: B 346 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5729 (tpt90) REVERT: B 374 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: B 434 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 461 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.1754 (tp) REVERT: B 487 ASN cc_start: 0.1914 (OUTLIER) cc_final: 0.1704 (p0) REVERT: B 489 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: B 740 MET cc_start: 0.9103 (tpp) cc_final: 0.8712 (tpp) REVERT: B 904 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: C 127 PHE cc_start: 0.8955 (t80) cc_final: 0.8466 (t80) REVERT: C 400 PHE cc_start: 0.8955 (p90) cc_final: 0.8475 (p90) REVERT: C 497 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.4795 (m-80) REVERT: C 633 TRP cc_start: 0.8821 (p90) cc_final: 0.8500 (p90) REVERT: C 731 MET cc_start: 0.8920 (ppp) cc_final: 0.8106 (ppp) REVERT: C 1029 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8714 (tpp) outliers start: 131 outliers final: 91 residues processed: 248 average time/residue: 0.1360 time to fit residues: 58.0210 Evaluate side-chains 226 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 122 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 212 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 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 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS 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 951 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1050 MET 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 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 540 ASN 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 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 951 VAL 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 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 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 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 546 LEU 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 734 THR 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 101 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 224 optimal weight: 0.1980 chunk 251 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 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** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046279 restraints weight = 136124.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047854 restraints weight = 76191.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048895 restraints weight = 51902.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049601 restraints weight = 40126.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050051 restraints weight = 33652.980| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26530 Z= 0.149 Angle : 0.711 14.793 36238 Z= 0.342 Chirality : 0.049 0.599 4254 Planarity : 0.004 0.054 4560 Dihedral : 7.726 105.339 4756 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.71 % Rotamer: Outliers : 3.92 % Allowed : 25.77 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.15), residues: 3162 helix: 1.60 (0.21), residues: 688 sheet: -0.90 (0.20), residues: 645 loop : -1.83 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.022 0.001 TYR B 453 PHE 0.018 0.001 PHE B 55 TRP 0.010 0.001 TRP A 104 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00339 (26428) covalent geometry : angle 0.66687 (35970) SS BOND : bond 0.00381 ( 38) SS BOND : angle 1.37113 ( 76) hydrogen bonds : bond 0.04125 ( 905) hydrogen bonds : angle 5.40440 ( 2499) link_BETA1-4 : bond 0.00395 ( 17) link_BETA1-4 : angle 2.11022 ( 51) link_NAG-ASN : bond 0.00525 ( 47) link_NAG-ASN : angle 3.69770 ( 141) *********************** 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 245 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 136 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8805 (tp) REVERT: A 53 ASP cc_start: 0.8892 (p0) cc_final: 0.8551 (p0) REVERT: A 55 PHE cc_start: 0.8735 (m-10) cc_final: 0.8367 (m-80) REVERT: A 175 PHE cc_start: 0.9245 (m-10) cc_final: 0.8968 (m-10) REVERT: A 191 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 402 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 495 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: A 664 ILE cc_start: 0.9456 (mt) cc_final: 0.9228 (mp) REVERT: A 740 MET cc_start: 0.9195 (tmm) cc_final: 0.8684 (ppp) REVERT: A 773 GLU cc_start: 0.8838 (tt0) cc_final: 0.8470 (tm-30) REVERT: A 900 MET cc_start: 0.9056 (pmm) cc_final: 0.8834 (pmm) REVERT: A 1002 GLN cc_start: 0.9216 (tt0) cc_final: 0.8891 (tm-30) REVERT: A 1029 MET cc_start: 0.8889 (tmm) cc_final: 0.8356 (tmm) REVERT: A 1039 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8690 (ptm160) REVERT: B 118 LEU cc_start: 0.8277 (tt) cc_final: 0.8071 (mp) REVERT: B 127 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: B 374 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: B 434 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 461 LEU cc_start: 0.3133 (OUTLIER) cc_final: 0.1813 (tp) REVERT: B 487 ASN cc_start: 0.1706 (OUTLIER) cc_final: 0.1439 (p0) REVERT: B 489 TYR cc_start: 0.5603 (OUTLIER) cc_final: 0.5364 (m-80) REVERT: B 740 MET cc_start: 0.9100 (tpp) cc_final: 0.8724 (tpp) REVERT: B 1111 GLU cc_start: 0.9032 (tp30) cc_final: 0.8575 (tm-30) REVERT: B 1129 VAL cc_start: 0.9165 (t) cc_final: 0.8921 (t) REVERT: C 92 PHE cc_start: 0.8894 (t80) cc_final: 0.8475 (t80) REVERT: C 127 PHE cc_start: 0.9002 (t80) cc_final: 0.8491 (t80) REVERT: C 170 TYR cc_start: 0.7700 (t80) cc_final: 0.7352 (t80) REVERT: C 497 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.4643 (m-80) REVERT: C 633 TRP cc_start: 0.8842 (p90) cc_final: 0.8302 (p90) REVERT: C 731 MET cc_start: 0.8952 (ppp) cc_final: 0.8112 (ppp) outliers start: 109 outliers final: 85 residues processed: 237 average time/residue: 0.1230 time to fit residues: 51.0418 Evaluate side-chains 225 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 129 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 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 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 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS 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 1050 MET 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 129 LYS 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 327 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 540 ASN 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 725 GLU 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 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 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 343 ASN Chi-restraints excluded: chain C residue 430 THR 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 546 LEU 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 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 171 optimal weight: 9.9990 chunk 236 optimal weight: 0.0030 chunk 2 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 254 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 overall best weight: 3.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 121 ASN ** 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 = 0.3459 r_free = 0.3459 target = 0.063053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045157 restraints weight = 136739.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046665 restraints weight = 76651.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047675 restraints weight = 52348.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048355 restraints weight = 40461.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048802 restraints weight = 33953.761| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 26530 Z= 0.215 Angle : 0.748 14.710 36238 Z= 0.363 Chirality : 0.049 0.591 4254 Planarity : 0.005 0.052 4560 Dihedral : 7.863 106.223 4756 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.08 % Favored : 90.86 % Rotamer: Outliers : 4.00 % Allowed : 25.88 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.15), residues: 3162 helix: 1.50 (0.21), residues: 693 sheet: -0.86 (0.21), residues: 631 loop : -1.89 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 328 TYR 0.019 0.002 TYR B 453 PHE 0.021 0.002 PHE B 127 TRP 0.009 0.001 TRP A 104 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00477 (26428) covalent geometry : angle 0.70678 (35970) SS BOND : bond 0.00525 ( 38) SS BOND : angle 1.31956 ( 76) hydrogen bonds : bond 0.04325 ( 905) hydrogen bonds : angle 5.47541 ( 2499) link_BETA1-4 : bond 0.00321 ( 17) link_BETA1-4 : angle 2.13719 ( 51) link_NAG-ASN : bond 0.00553 ( 47) link_NAG-ASN : angle 3.70761 ( 141) *********************** 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 238 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 127 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 53 ASP cc_start: 0.8965 (p0) cc_final: 0.8615 (p0) REVERT: A 55 PHE cc_start: 0.8777 (m-10) cc_final: 0.8371 (m-80) REVERT: A 175 PHE cc_start: 0.9278 (m-10) cc_final: 0.9017 (m-10) REVERT: A 191 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 402 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8865 (tp) REVERT: A 664 ILE cc_start: 0.9472 (mt) cc_final: 0.9245 (mp) REVERT: A 759 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8544 (t80) REVERT: A 773 GLU cc_start: 0.8858 (tt0) cc_final: 0.8484 (tm-30) REVERT: A 1002 GLN cc_start: 0.9271 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 1029 MET cc_start: 0.8905 (tmm) cc_final: 0.8357 (tmm) REVERT: A 1039 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7889 (ptm160) REVERT: B 118 LEU cc_start: 0.8458 (tt) cc_final: 0.8232 (mp) REVERT: B 127 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: B 170 TYR cc_start: 0.7497 (t80) cc_final: 0.7116 (t80) REVERT: B 374 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: B 434 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 461 LEU cc_start: 0.3040 (OUTLIER) cc_final: 0.1715 (tp) REVERT: B 487 ASN cc_start: 0.2165 (OUTLIER) cc_final: 0.1940 (p0) REVERT: B 740 MET cc_start: 0.9111 (tpp) cc_final: 0.8785 (tpp) REVERT: B 900 MET cc_start: 0.8996 (mmp) cc_final: 0.8709 (mmt) REVERT: B 904 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: B 1129 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8974 (t) REVERT: C 92 PHE cc_start: 0.8920 (t80) cc_final: 0.8487 (t80) REVERT: C 127 PHE cc_start: 0.9007 (t80) cc_final: 0.8467 (t80) REVERT: C 497 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: C 633 TRP cc_start: 0.8885 (p90) cc_final: 0.8492 (p90) REVERT: C 731 MET cc_start: 0.8925 (ppp) cc_final: 0.8077 (ppp) REVERT: C 740 MET cc_start: 0.9027 (tpp) cc_final: 0.8780 (tpp) outliers start: 111 outliers final: 88 residues processed: 226 average time/residue: 0.1407 time to fit residues: 54.7180 Evaluate side-chains 221 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 121 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 212 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 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 415 THR 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 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS 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 759 PHE 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 1111 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 25 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 129 LYS 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 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 434 ILE 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 540 ASN 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 725 GLU 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 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 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 343 ASN Chi-restraints excluded: chain C residue 430 THR 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 546 LEU 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 734 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 65 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 260 optimal weight: 0.0870 chunk 141 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046945 restraints weight = 133214.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048559 restraints weight = 72963.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049622 restraints weight = 49103.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050352 restraints weight = 37542.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050847 restraints weight = 31215.890| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26530 Z= 0.116 Angle : 0.710 14.766 36238 Z= 0.338 Chirality : 0.049 0.613 4254 Planarity : 0.004 0.063 4560 Dihedral : 7.501 105.187 4756 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 2.88 % Allowed : 27.11 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 3162 helix: 1.65 (0.21), residues: 692 sheet: -0.86 (0.21), residues: 641 loop : -1.80 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1019 TYR 0.021 0.001 TYR A 265 PHE 0.025 0.001 PHE B 216 TRP 0.014 0.001 TRP A 104 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00260 (26428) covalent geometry : angle 0.66837 (35970) SS BOND : bond 0.00469 ( 38) SS BOND : angle 1.16703 ( 76) hydrogen bonds : bond 0.03951 ( 905) hydrogen bonds : angle 5.26041 ( 2499) link_BETA1-4 : bond 0.00452 ( 17) link_BETA1-4 : angle 2.07551 ( 51) link_NAG-ASN : bond 0.00541 ( 47) link_NAG-ASN : angle 3.66831 ( 141) ********************** 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: 80 poor density : 147 time to evaluate : 0.925 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: 0.9071 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 175 PHE cc_start: 0.9227 (m-10) cc_final: 0.8986 (m-10) REVERT: A 191 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 357 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7695 (tpp-160) REVERT: A 402 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 495 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.3370 (m-80) REVERT: A 632 THR cc_start: 0.9023 (m) cc_final: 0.8813 (p) REVERT: A 664 ILE cc_start: 0.9425 (mt) cc_final: 0.9173 (mp) REVERT: A 773 GLU cc_start: 0.8807 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 1002 GLN cc_start: 0.9226 (tt0) cc_final: 0.8834 (tm-30) REVERT: A 1029 MET cc_start: 0.8875 (tmm) cc_final: 0.8302 (tmm) REVERT: B 127 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: B 170 TYR cc_start: 0.7458 (t80) cc_final: 0.7125 (t80) REVERT: B 374 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: B 461 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.1547 (tp) REVERT: B 740 MET cc_start: 0.9048 (tpp) cc_final: 0.8802 (tpp) REVERT: B 900 MET cc_start: 0.8974 (mmp) cc_final: 0.8763 (mmt) REVERT: B 904 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: B 1111 GLU cc_start: 0.9050 (tp30) cc_final: 0.8607 (tm-30) REVERT: B 1129 VAL cc_start: 0.9204 (t) cc_final: 0.8969 (t) REVERT: C 92 PHE cc_start: 0.8837 (t80) cc_final: 0.8491 (t80) REVERT: C 127 PHE cc_start: 0.8946 (t80) cc_final: 0.8400 (t80) REVERT: C 170 TYR cc_start: 0.7765 (t80) cc_final: 0.7405 (t80) REVERT: C 423 TYR cc_start: 0.7332 (t80) cc_final: 0.7099 (t80) REVERT: C 633 TRP cc_start: 0.8863 (p90) cc_final: 0.8152 (p90) REVERT: C 731 MET cc_start: 0.8936 (ppp) cc_final: 0.8140 (ppp) REVERT: C 740 MET cc_start: 0.8984 (tpp) cc_final: 0.8411 (tpp) outliers start: 80 outliers final: 66 residues processed: 222 average time/residue: 0.1329 time to fit residues: 50.8594 Evaluate side-chains 206 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 389 ASP 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 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS 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 1039 ARG 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 240 THR 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 540 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU 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 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1076 THR 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 343 ASN Chi-restraints excluded: chain C residue 430 THR 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 546 LEU 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 734 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 288 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 245 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 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** ** C1048 HIS ** 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 = 0.3493 r_free = 0.3493 target = 0.064378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046316 restraints weight = 135505.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047845 restraints weight = 76563.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048848 restraints weight = 52621.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049518 restraints weight = 40868.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049972 restraints weight = 34565.366| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26530 Z= 0.141 Angle : 0.708 14.682 36238 Z= 0.337 Chirality : 0.048 0.600 4254 Planarity : 0.004 0.053 4560 Dihedral : 7.449 103.926 4756 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.56 % Rotamer: Outliers : 2.95 % Allowed : 27.32 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3162 helix: 1.65 (0.21), residues: 692 sheet: -0.83 (0.21), residues: 622 loop : -1.78 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.021 0.001 TYR A 265 PHE 0.027 0.001 PHE A 592 TRP 0.043 0.001 TRP A 633 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00321 (26428) covalent geometry : angle 0.66582 (35970) SS BOND : bond 0.00371 ( 38) SS BOND : angle 1.18641 ( 76) hydrogen bonds : bond 0.03941 ( 905) hydrogen bonds : angle 5.28229 ( 2499) link_BETA1-4 : bond 0.00358 ( 17) link_BETA1-4 : angle 2.06720 ( 51) link_NAG-ASN : bond 0.00512 ( 47) link_NAG-ASN : angle 3.65041 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.92 seconds wall clock time: 74 minutes 17.19 seconds (4457.19 seconds total)