Starting phenix.real_space_refine on Sat May 24 21:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.map" model { file = "/net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x56_38064/05_2025/8x56_38064.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16422 2.51 5 N 4197 2.21 5 O 5016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25749 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} 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: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} 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: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} 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: "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: 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: "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: 14.23, per 1000 atoms: 0.55 Number of scatterers: 25749 At special positions: 0 Unit cell: (143.52, 142.48, 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 5016 8.00 N 4197 7.00 C 16422 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 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=2.02 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=2.03 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=1, 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-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 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 E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 282 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 3.2 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 25.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 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: 3.647A 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: 3.968A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.858A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.703A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.790A 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: 3.594A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.855A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A 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: 4.991A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) 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: 3.550A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.876A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.598A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.829A 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: 4.361A 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 removed outlier: 3.623A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.510A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.050A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) 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: 3.620A 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: 3.649A pdb=" N VAL C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.942A 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 618 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.408A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.581A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) 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: 4.436A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.742A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.502A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) 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: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.452A 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: 7.277A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.845A 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: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.621A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.172A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.764A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.038A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.932A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.914A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.863A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.629A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.811A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.844A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.207A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.198A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.586A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.577A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.999A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.698A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.311A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.239A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.847A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.951A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.964A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.590A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.548A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.601A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.378A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.527A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.520A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.081A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.507A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.542A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.589A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.104A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.542A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.638A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.608A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.814A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 891 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.77 Time building geometry restraints manager: 7.46 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: 8118 1.34 - 1.47: 6745 1.47 - 1.60: 11345 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 26349 Sorted by residual: bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.30e+01 bond pdb=" N ILE C 212 " pdb=" CA ILE C 212 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" N ILE C 210 " pdb=" CA ILE C 210 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.91e+00 bond pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 1.462 1.489 -0.028 9.30e-03 1.16e+04 8.79e+00 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 34587 1.97 - 3.95: 1027 3.95 - 5.92: 186 5.92 - 7.90: 48 7.90 - 9.87: 8 Bond angle restraints: 35856 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.46 6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" N LEU B 387 " pdb=" CA LEU B 387 " pdb=" C LEU B 387 " ideal model delta sigma weight residual 114.62 108.81 5.81 1.14e+00 7.69e-01 2.60e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 115.59 6.31 1.26e+00 6.30e-01 2.50e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 112.96 108.46 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 115.89 110.37 5.52 1.32e+00 5.74e-01 1.75e+01 ... (remaining 35851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 14604 23.08 - 46.16: 1421 46.16 - 69.24: 162 69.24 - 92.32: 143 92.32 - 115.40: 113 Dihedral angle restraints: 16443 sinusoidal: 7167 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.82 83.18 1 1.00e+01 1.00e-02 8.46e+01 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 93.00 26.01 66.99 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 33.06 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4185 0.180 - 0.360: 32 0.360 - 0.540: 0 0.540 - 0.721: 0 0.721 - 0.901: 3 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 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 4217 not shown) Planarity restraints: 4598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO A 82 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 217 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 237 " 0.288 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG C 237 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 237 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 237 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 237 " 0.009 2.00e-02 2.50e+03 ... (remaining 4595 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 449 2.63 - 3.20: 23986 3.20 - 3.77: 40142 3.77 - 4.33: 53976 4.33 - 4.90: 87247 Nonbonded interactions: 205800 Sorted by model distance: nonbonded pdb=" OD1 ASN B 532 " pdb=" N LEU B 533 " model vdw 2.064 3.120 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.115 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" O7 NAG C1301 " model vdw 2.138 3.040 nonbonded pdb=" NE2 GLN C 173 " pdb=" O PRO C 174 " model vdw 2.138 3.120 nonbonded pdb=" O ASN B 978 " pdb=" OG1 THR C 547 " model vdw 2.148 3.040 ... (remaining 205795 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' 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' } 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: 1.700 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: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 58.340 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 0.049 26447 Z= 0.228 Angle : 0.867 18.118 36109 Z= 0.438 Chirality : 0.056 0.901 4220 Planarity : 0.006 0.129 4554 Dihedral : 21.396 115.405 10371 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.96 % Favored : 92.85 % Rotamer: Outliers : 0.58 % Allowed : 27.32 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 3159 helix: 0.91 (0.20), residues: 699 sheet: -0.93 (0.21), residues: 584 loop : -2.04 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 633 HIS 0.010 0.001 HIS C 339 PHE 0.034 0.001 PHE C 342 TYR 0.023 0.001 TYR A 365 ARG 0.006 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 44) link_NAG-ASN : angle 4.91707 ( 132) link_BETA1-4 : bond 0.00478 ( 15) link_BETA1-4 : angle 2.37167 ( 45) hydrogen bonds : bond 0.20853 ( 887) hydrogen bonds : angle 8.35984 ( 2466) SS BOND : bond 0.00464 ( 38) SS BOND : angle 1.71028 ( 76) covalent geometry : bond 0.00422 (26349) covalent geometry : angle 0.80896 (35856) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8885 (mmm) cc_final: 0.8585 (mmp) REVERT: A 896 ILE cc_start: 0.8637 (tp) cc_final: 0.8075 (tt) REVERT: A 1050 MET cc_start: 0.7898 (ptp) cc_final: 0.7559 (ptp) REVERT: A 1107 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7343 (mmt-90) REVERT: B 377 PHE cc_start: 0.7024 (t80) cc_final: 0.6746 (t80) REVERT: B 985 ASP cc_start: 0.7608 (p0) cc_final: 0.7390 (p0) REVERT: C 699 LEU cc_start: 0.8592 (mt) cc_final: 0.8363 (mp) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.3413 time to fit residues: 103.8829 Evaluate side-chains 160 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 0.0770 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 30.0000 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 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 = 0.3823 r_free = 0.3823 target = 0.093374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066836 restraints weight = 93552.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068773 restraints weight = 58562.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069756 restraints weight = 38171.578| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26447 Z= 0.183 Angle : 0.792 17.093 36109 Z= 0.376 Chirality : 0.051 0.655 4220 Planarity : 0.005 0.071 4554 Dihedral : 14.947 107.852 4663 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 3.14 % Allowed : 24.25 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3159 helix: 1.00 (0.20), residues: 716 sheet: -0.99 (0.20), residues: 624 loop : -1.94 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 633 HIS 0.005 0.001 HIS A 625 PHE 0.014 0.001 PHE C1042 TYR 0.026 0.002 TYR B 204 ARG 0.005 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 44) link_NAG-ASN : angle 4.82600 ( 132) link_BETA1-4 : bond 0.00268 ( 15) link_BETA1-4 : angle 3.47800 ( 45) hydrogen bonds : bond 0.04883 ( 887) hydrogen bonds : angle 6.28816 ( 2466) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.55555 ( 76) covalent geometry : bond 0.00411 (26349) covalent geometry : angle 0.72478 (35856) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 156 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 127 PHE cc_start: 0.8207 (t80) cc_final: 0.7835 (t80) REVERT: A 177 MET cc_start: 0.5710 (mmt) cc_final: 0.3417 (tmm) REVERT: A 220 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6266 (t80) REVERT: A 896 ILE cc_start: 0.8800 (tp) cc_final: 0.8283 (tt) REVERT: B 102 ARG cc_start: 0.3803 (ptt180) cc_final: 0.3464 (ptt-90) REVERT: B 164 ASN cc_start: 0.6031 (OUTLIER) cc_final: 0.5491 (p0) REVERT: B 200 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6688 (t80) REVERT: B 204 TYR cc_start: 0.7454 (m-10) cc_final: 0.6938 (m-10) REVERT: B 697 MET cc_start: 0.8371 (mmt) cc_final: 0.8150 (tpt) REVERT: B 869 MET cc_start: 0.8821 (pmm) cc_final: 0.8581 (pmm) REVERT: B 904 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: C 173 GLN cc_start: 0.6976 (tp-100) cc_final: 0.6775 (tp-100) REVERT: C 378 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9277 (mmmt) REVERT: C 726 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8520 (mm) REVERT: C 756 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7374 (t80) REVERT: C 816 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7232 (m) REVERT: C 1029 MET cc_start: 0.8786 (tpp) cc_final: 0.8553 (tpp) outliers start: 87 outliers final: 42 residues processed: 227 average time/residue: 0.3273 time to fit residues: 124.5721 Evaluate side-chains 185 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 25 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 293 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 926 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.094108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067776 restraints weight = 93460.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069954 restraints weight = 57904.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070674 restraints weight = 36835.757| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26447 Z= 0.135 Angle : 0.724 16.432 36109 Z= 0.341 Chirality : 0.050 0.613 4220 Planarity : 0.005 0.067 4554 Dihedral : 10.133 108.385 4656 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 4.04 % Allowed : 23.53 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3159 helix: 1.07 (0.20), residues: 722 sheet: -1.08 (0.20), residues: 612 loop : -1.90 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C 339 PHE 0.026 0.001 PHE A 562 TYR 0.015 0.001 TYR A 837 ARG 0.003 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 44) link_NAG-ASN : angle 4.64441 ( 132) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 3.28416 ( 45) hydrogen bonds : bond 0.04204 ( 887) hydrogen bonds : angle 5.74598 ( 2466) SS BOND : bond 0.00376 ( 38) SS BOND : angle 1.41975 ( 76) covalent geometry : bond 0.00304 (26349) covalent geometry : angle 0.65640 (35856) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 161 time to evaluate : 2.960 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 127 PHE cc_start: 0.8231 (t80) cc_final: 0.7827 (t80) REVERT: A 177 MET cc_start: 0.5656 (mmt) cc_final: 0.3680 (tmm) REVERT: A 188 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6862 (p0) REVERT: A 392 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: B 102 ARG cc_start: 0.4283 (ptt180) cc_final: 0.3866 (mtt180) REVERT: B 164 ASN cc_start: 0.6075 (OUTLIER) cc_final: 0.5542 (p0) REVERT: B 200 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 204 TYR cc_start: 0.7513 (m-10) cc_final: 0.6920 (m-10) REVERT: B 869 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7903 (pmm) REVERT: B 904 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.7059 (m-10) REVERT: C 173 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6669 (tp-100) REVERT: C 378 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9264 (mmmt) REVERT: C 393 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7929 (t) REVERT: C 756 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 1017 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 112 outliers final: 64 residues processed: 257 average time/residue: 0.3224 time to fit residues: 138.4370 Evaluate side-chains 207 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 135 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 321 GLN A 414 GLN A 777 ASN A1108 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 437 ASN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.088100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060745 restraints weight = 97054.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062487 restraints weight = 56552.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063201 restraints weight = 36423.622| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 26447 Z= 0.302 Angle : 0.825 16.563 36109 Z= 0.404 Chirality : 0.052 0.646 4220 Planarity : 0.005 0.078 4554 Dihedral : 8.511 106.030 4654 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.12 % Favored : 90.79 % Rotamer: Outliers : 5.55 % Allowed : 23.60 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 3159 helix: 0.76 (0.20), residues: 717 sheet: -0.98 (0.21), residues: 587 loop : -2.04 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 633 HIS 0.010 0.001 HIS B 49 PHE 0.022 0.002 PHE B 927 TYR 0.024 0.002 TYR B 495 ARG 0.009 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 44) link_NAG-ASN : angle 4.69850 ( 132) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 3.25922 ( 45) hydrogen bonds : bond 0.04950 ( 887) hydrogen bonds : angle 5.90812 ( 2466) SS BOND : bond 0.00532 ( 38) SS BOND : angle 1.83922 ( 76) covalent geometry : bond 0.00675 (26349) covalent geometry : angle 0.76450 (35856) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 132 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 105 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8859 (mm) REVERT: A 177 MET cc_start: 0.5839 (mmt) cc_final: 0.3391 (tmm) REVERT: A 191 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: A 630 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 1031 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7262 (tt0) REVERT: A 1034 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8878 (tp) REVERT: A 1108 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8413 (m-40) REVERT: B 55 PHE cc_start: 0.7275 (m-10) cc_final: 0.7030 (m-10) REVERT: B 164 ASN cc_start: 0.5939 (OUTLIER) cc_final: 0.5522 (p0) REVERT: B 200 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 869 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.7993 (pmm) REVERT: B 996 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9214 (mm) REVERT: B 1029 MET cc_start: 0.9140 (tpp) cc_final: 0.8168 (tpp) REVERT: C 102 ARG cc_start: 0.5659 (mtt180) cc_final: 0.5412 (mtt180) REVERT: C 177 MET cc_start: 0.6074 (mmp) cc_final: 0.5860 (mmp) REVERT: C 378 LYS cc_start: 0.9502 (mmmt) cc_final: 0.9280 (mmmt) REVERT: C 532 ASN cc_start: 0.9079 (t0) cc_final: 0.8710 (t0) REVERT: C 756 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7588 (t80) REVERT: C 816 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7636 (m) REVERT: C 1005 GLN cc_start: 0.8726 (tp40) cc_final: 0.8485 (tp40) REVERT: C 1017 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8050 (tm-30) outliers start: 154 outliers final: 91 residues processed: 267 average time/residue: 0.3439 time to fit residues: 150.2936 Evaluate side-chains 219 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 117 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 195 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062716 restraints weight = 95936.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064870 restraints weight = 55470.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065395 restraints weight = 34389.194| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26447 Z= 0.148 Angle : 0.715 15.292 36109 Z= 0.343 Chirality : 0.049 0.612 4220 Planarity : 0.005 0.052 4554 Dihedral : 7.939 103.447 4654 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 4.97 % Allowed : 24.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 3159 helix: 1.05 (0.20), residues: 717 sheet: -1.06 (0.20), residues: 646 loop : -2.01 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.005 0.001 HIS C 339 PHE 0.026 0.001 PHE B 592 TYR 0.022 0.001 TYR A 369 ARG 0.011 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 44) link_NAG-ASN : angle 4.50557 ( 132) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 2.74074 ( 45) hydrogen bonds : bond 0.04149 ( 887) hydrogen bonds : angle 5.52103 ( 2466) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.50217 ( 76) covalent geometry : bond 0.00335 (26349) covalent geometry : angle 0.65277 (35856) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 141 time to evaluate : 2.623 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 127 PHE cc_start: 0.8767 (t80) cc_final: 0.8122 (t80) REVERT: A 177 MET cc_start: 0.5802 (mmt) cc_final: 0.3757 (tmm) REVERT: A 191 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: A 220 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 630 THR cc_start: 0.8245 (m) cc_final: 0.8036 (p) REVERT: A 1031 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7408 (tt0) REVERT: A 1034 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8846 (tp) REVERT: B 54 LEU cc_start: 0.8846 (mm) cc_final: 0.8362 (tp) REVERT: B 102 ARG cc_start: 0.3697 (ptt180) cc_final: 0.2895 (mtt90) REVERT: B 164 ASN cc_start: 0.6226 (OUTLIER) cc_final: 0.5755 (p0) REVERT: B 204 TYR cc_start: 0.7587 (m-10) cc_final: 0.7020 (m-10) REVERT: B 740 MET cc_start: 0.7788 (tpt) cc_final: 0.7547 (tpt) REVERT: B 869 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8077 (pmm) REVERT: B 985 ASP cc_start: 0.8143 (p0) cc_final: 0.7844 (p0) REVERT: C 102 ARG cc_start: 0.5647 (mtt180) cc_final: 0.5431 (mtt180) REVERT: C 378 LYS cc_start: 0.9509 (mmmt) cc_final: 0.9279 (mmmt) REVERT: C 385 THR cc_start: 0.8500 (m) cc_final: 0.8283 (p) REVERT: C 441 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6850 (tt) REVERT: C 532 ASN cc_start: 0.9066 (t0) cc_final: 0.8712 (t0) REVERT: C 592 PHE cc_start: 0.6276 (t80) cc_final: 0.6058 (t80) REVERT: C 756 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 759 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 816 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7655 (m) REVERT: C 1017 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8145 (tm-30) outliers start: 138 outliers final: 89 residues processed: 261 average time/residue: 0.3110 time to fit residues: 137.2354 Evaluate side-chains 226 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 128 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062524 restraints weight = 95744.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064073 restraints weight = 55989.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064853 restraints weight = 37458.909| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26447 Z= 0.160 Angle : 0.706 15.429 36109 Z= 0.338 Chirality : 0.049 0.608 4220 Planarity : 0.005 0.052 4554 Dihedral : 7.638 103.047 4653 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.79 % Favored : 92.12 % Rotamer: Outliers : 5.08 % Allowed : 24.22 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3159 helix: 1.15 (0.20), residues: 711 sheet: -1.04 (0.20), residues: 663 loop : -1.99 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.006 0.001 HIS C 339 PHE 0.020 0.001 PHE B 592 TYR 0.018 0.001 TYR A 369 ARG 0.007 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 44) link_NAG-ASN : angle 4.41912 ( 132) link_BETA1-4 : bond 0.00277 ( 15) link_BETA1-4 : angle 2.54114 ( 45) hydrogen bonds : bond 0.04050 ( 887) hydrogen bonds : angle 5.36806 ( 2466) SS BOND : bond 0.00476 ( 38) SS BOND : angle 1.41179 ( 76) covalent geometry : bond 0.00363 (26349) covalent geometry : angle 0.64621 (35856) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 134 time to evaluate : 2.619 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 177 MET cc_start: 0.5815 (mmt) cc_final: 0.3731 (tmm) REVERT: A 191 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 220 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6400 (t80) REVERT: A 495 TYR cc_start: 0.3944 (OUTLIER) cc_final: 0.3683 (m-80) REVERT: A 630 THR cc_start: 0.8222 (m) cc_final: 0.7913 (m) REVERT: B 54 LEU cc_start: 0.8891 (mm) cc_final: 0.8570 (mt) REVERT: B 102 ARG cc_start: 0.3591 (ptt180) cc_final: 0.2832 (mtt90) REVERT: B 164 ASN cc_start: 0.6232 (OUTLIER) cc_final: 0.5813 (p0) REVERT: B 204 TYR cc_start: 0.7471 (m-10) cc_final: 0.6919 (m-10) REVERT: B 495 TYR cc_start: -0.0010 (OUTLIER) cc_final: -0.1038 (t80) REVERT: B 869 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.7911 (pmm) REVERT: B 974 SER cc_start: 0.9040 (t) cc_final: 0.8468 (m) REVERT: B 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8957 (tpp) REVERT: C 177 MET cc_start: 0.6305 (mmp) cc_final: 0.6085 (mmp) REVERT: C 328 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5879 (ttp80) REVERT: C 378 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9281 (mmmt) REVERT: C 441 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7002 (tt) REVERT: C 532 ASN cc_start: 0.9085 (t0) cc_final: 0.8458 (p0) REVERT: C 636 TYR cc_start: 0.7381 (t80) cc_final: 0.7133 (t80) REVERT: C 756 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7517 (t80) outliers start: 141 outliers final: 98 residues processed: 257 average time/residue: 0.3118 time to fit residues: 135.4696 Evaluate side-chains 239 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 132 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR 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 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 13 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 154 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 201 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062412 restraints weight = 96133.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064905 restraints weight = 58454.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065750 restraints weight = 35169.870| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26447 Z= 0.132 Angle : 0.697 15.079 36109 Z= 0.331 Chirality : 0.048 0.608 4220 Planarity : 0.004 0.052 4554 Dihedral : 7.441 100.399 4653 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 4.76 % Allowed : 24.61 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3159 helix: 1.27 (0.20), residues: 708 sheet: -0.93 (0.20), residues: 662 loop : -1.96 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.007 0.001 HIS C 339 PHE 0.021 0.001 PHE A 562 TYR 0.020 0.001 TYR C 170 ARG 0.006 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 44) link_NAG-ASN : angle 4.33756 ( 132) link_BETA1-4 : bond 0.00319 ( 15) link_BETA1-4 : angle 2.42052 ( 45) hydrogen bonds : bond 0.03870 ( 887) hydrogen bonds : angle 5.22987 ( 2466) SS BOND : bond 0.00459 ( 38) SS BOND : angle 1.49756 ( 76) covalent geometry : bond 0.00301 (26349) covalent geometry : angle 0.63847 (35856) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 142 time to evaluate : 2.585 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 105 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 127 PHE cc_start: 0.8777 (t80) cc_final: 0.8179 (t80) REVERT: A 177 MET cc_start: 0.5644 (mmt) cc_final: 0.3699 (tmm) REVERT: A 191 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: A 220 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.6243 (t80) REVERT: A 495 TYR cc_start: 0.3944 (OUTLIER) cc_final: 0.3675 (m-80) REVERT: A 630 THR cc_start: 0.8146 (m) cc_final: 0.7878 (m) REVERT: A 697 MET cc_start: 0.8676 (mmm) cc_final: 0.8225 (mmm) REVERT: A 740 MET cc_start: 0.8658 (ttp) cc_final: 0.7656 (ttp) REVERT: B 54 LEU cc_start: 0.8902 (mm) cc_final: 0.8578 (mt) REVERT: B 102 ARG cc_start: 0.3747 (ptt180) cc_final: 0.3010 (mtt90) REVERT: B 164 ASN cc_start: 0.6196 (OUTLIER) cc_final: 0.5747 (p0) REVERT: B 204 TYR cc_start: 0.7370 (m-10) cc_final: 0.6851 (m-10) REVERT: B 495 TYR cc_start: 0.0315 (OUTLIER) cc_final: -0.0754 (t80) REVERT: B 869 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8019 (pmm) REVERT: B 974 SER cc_start: 0.9019 (t) cc_final: 0.8480 (m) REVERT: C 177 MET cc_start: 0.6565 (mmp) cc_final: 0.6311 (mmp) REVERT: C 328 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5908 (ttp80) REVERT: C 378 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9277 (mmmt) REVERT: C 441 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6954 (tt) REVERT: C 532 ASN cc_start: 0.9080 (t0) cc_final: 0.8507 (p0) REVERT: C 756 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7470 (t80) REVERT: C 816 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7733 (m) REVERT: C 973 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8188 (tp) outliers start: 132 outliers final: 95 residues processed: 258 average time/residue: 0.3070 time to fit residues: 132.7497 Evaluate side-chains 240 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 133 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR 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 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 311 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062873 restraints weight = 96893.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065140 restraints weight = 60140.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065703 restraints weight = 39637.318| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26447 Z= 0.130 Angle : 0.690 15.044 36109 Z= 0.326 Chirality : 0.048 0.608 4220 Planarity : 0.004 0.052 4554 Dihedral : 7.276 99.732 4653 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 4.36 % Allowed : 25.08 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 3159 helix: 1.34 (0.20), residues: 707 sheet: -0.88 (0.20), residues: 662 loop : -1.92 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.008 0.001 HIS C 339 PHE 0.039 0.001 PHE B 592 TYR 0.016 0.001 TYR A 369 ARG 0.005 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 44) link_NAG-ASN : angle 4.24871 ( 132) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 2.31848 ( 45) hydrogen bonds : bond 0.03759 ( 887) hydrogen bonds : angle 5.13842 ( 2466) SS BOND : bond 0.00383 ( 38) SS BOND : angle 1.45386 ( 76) covalent geometry : bond 0.00294 (26349) covalent geometry : angle 0.63353 (35856) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 140 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: A 495 TYR cc_start: 0.3990 (OUTLIER) cc_final: 0.3672 (m-80) REVERT: A 630 THR cc_start: 0.8108 (m) cc_final: 0.7847 (m) REVERT: A 896 ILE cc_start: 0.8992 (tp) cc_final: 0.8773 (tp) REVERT: B 54 LEU cc_start: 0.8999 (mm) cc_final: 0.8678 (mt) REVERT: B 102 ARG cc_start: 0.3855 (ptt180) cc_final: 0.3135 (mtt90) REVERT: B 164 ASN cc_start: 0.6422 (OUTLIER) cc_final: 0.5979 (p0) REVERT: B 200 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7117 (t80) REVERT: B 204 TYR cc_start: 0.7484 (m-10) cc_final: 0.6971 (m-10) REVERT: B 332 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 495 TYR cc_start: 0.0377 (OUTLIER) cc_final: -0.0852 (t80) REVERT: B 869 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7879 (pmm) REVERT: B 974 SER cc_start: 0.8993 (t) cc_final: 0.8472 (m) REVERT: B 1029 MET cc_start: 0.9235 (tpp) cc_final: 0.8962 (tpp) REVERT: C 177 MET cc_start: 0.6709 (mmp) cc_final: 0.6392 (mmp) REVERT: C 328 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5582 (ttp80) REVERT: C 378 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9285 (mmmt) REVERT: C 441 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6968 (tt) REVERT: C 532 ASN cc_start: 0.9094 (t0) cc_final: 0.8519 (p0) REVERT: C 756 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 816 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7775 (m) REVERT: C 973 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8153 (tp) outliers start: 121 outliers final: 93 residues processed: 246 average time/residue: 0.3265 time to fit residues: 134.2758 Evaluate side-chains 234 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 129 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR 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 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 195 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.087676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.060241 restraints weight = 97155.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062455 restraints weight = 58005.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062898 restraints weight = 35156.571| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26447 Z= 0.228 Angle : 0.758 16.005 36109 Z= 0.366 Chirality : 0.050 0.617 4220 Planarity : 0.005 0.055 4554 Dihedral : 7.497 105.114 4653 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.96 % Favored : 90.95 % Rotamer: Outliers : 4.54 % Allowed : 25.41 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3159 helix: 1.05 (0.20), residues: 715 sheet: -0.91 (0.21), residues: 623 loop : -1.96 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 104 HIS 0.007 0.001 HIS B 49 PHE 0.032 0.002 PHE A 592 TYR 0.022 0.002 TYR C 170 ARG 0.007 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 44) link_NAG-ASN : angle 4.27171 ( 132) link_BETA1-4 : bond 0.00240 ( 15) link_BETA1-4 : angle 2.45002 ( 45) hydrogen bonds : bond 0.04351 ( 887) hydrogen bonds : angle 5.39665 ( 2466) SS BOND : bond 0.00478 ( 38) SS BOND : angle 1.75240 ( 76) covalent geometry : bond 0.00517 (26349) covalent geometry : angle 0.70484 (35856) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 130 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8907 (t80) cc_final: 0.8274 (t80) REVERT: A 630 THR cc_start: 0.8120 (m) cc_final: 0.7836 (m) REVERT: A 731 MET cc_start: 0.9097 (ptp) cc_final: 0.8717 (ptp) REVERT: A 981 LEU cc_start: 0.8670 (tp) cc_final: 0.8279 (pp) REVERT: A 1107 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7488 (mmt-90) REVERT: B 54 LEU cc_start: 0.9010 (mm) cc_final: 0.8667 (mt) REVERT: B 102 ARG cc_start: 0.3704 (ptt180) cc_final: 0.2971 (mtt90) REVERT: B 164 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6004 (p0) REVERT: B 200 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 204 TYR cc_start: 0.7360 (m-10) cc_final: 0.6701 (m-10) REVERT: B 332 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 495 TYR cc_start: 0.0844 (OUTLIER) cc_final: 0.0014 (t80) REVERT: B 768 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9125 (p) REVERT: B 869 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8043 (pmm) REVERT: B 974 SER cc_start: 0.9063 (t) cc_final: 0.8540 (m) REVERT: C 177 MET cc_start: 0.7098 (mmp) cc_final: 0.6816 (mmp) REVERT: C 378 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9288 (mmmt) REVERT: C 441 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6919 (tt) REVERT: C 532 ASN cc_start: 0.9137 (t0) cc_final: 0.8673 (p0) REVERT: C 756 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 816 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7852 (m) outliers start: 126 outliers final: 106 residues processed: 240 average time/residue: 0.3167 time to fit residues: 127.8251 Evaluate side-chains 242 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 127 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 81 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 255 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.089649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062720 restraints weight = 95917.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065031 restraints weight = 59026.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065797 restraints weight = 36304.947| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26447 Z= 0.120 Angle : 0.703 14.991 36109 Z= 0.332 Chirality : 0.049 0.616 4220 Planarity : 0.004 0.051 4554 Dihedral : 7.283 101.675 4653 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.12 % Favored : 92.78 % Rotamer: Outliers : 3.39 % Allowed : 26.59 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3159 helix: 1.30 (0.20), residues: 709 sheet: -0.85 (0.20), residues: 630 loop : -1.90 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.008 0.001 HIS C 339 PHE 0.025 0.001 PHE B 92 TYR 0.015 0.001 TYR A 369 ARG 0.006 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 44) link_NAG-ASN : angle 4.12403 ( 132) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 2.15667 ( 45) hydrogen bonds : bond 0.03774 ( 887) hydrogen bonds : angle 5.13631 ( 2466) SS BOND : bond 0.00399 ( 38) SS BOND : angle 1.46465 ( 76) covalent geometry : bond 0.00271 (26349) covalent geometry : angle 0.65138 (35856) Misc. bond : bond 0.00063 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 144 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 127 PHE cc_start: 0.8787 (t80) cc_final: 0.8241 (t80) REVERT: A 177 MET cc_start: 0.6410 (mmp) cc_final: 0.4676 (ptt) REVERT: A 191 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 630 THR cc_start: 0.8040 (m) cc_final: 0.7756 (m) REVERT: A 731 MET cc_start: 0.8896 (ptp) cc_final: 0.8489 (ptp) REVERT: A 740 MET cc_start: 0.8295 (ttm) cc_final: 0.8018 (ttm) REVERT: A 896 ILE cc_start: 0.8999 (tp) cc_final: 0.8770 (tp) REVERT: A 1029 MET cc_start: 0.7825 (tpp) cc_final: 0.7621 (tpp) REVERT: B 54 LEU cc_start: 0.9001 (mm) cc_final: 0.8699 (mt) REVERT: B 102 ARG cc_start: 0.3797 (ptt180) cc_final: 0.3312 (mtt180) REVERT: B 164 ASN cc_start: 0.6197 (OUTLIER) cc_final: 0.5800 (p0) REVERT: B 200 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7394 (t80) REVERT: B 204 TYR cc_start: 0.7176 (m-10) cc_final: 0.6594 (m-10) REVERT: B 495 TYR cc_start: 0.0546 (OUTLIER) cc_final: -0.0424 (t80) REVERT: B 855 PHE cc_start: 0.7095 (t80) cc_final: 0.6840 (t80) REVERT: B 869 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7932 (pmm) REVERT: B 974 SER cc_start: 0.8982 (t) cc_final: 0.8515 (m) REVERT: B 1029 MET cc_start: 0.9203 (tpp) cc_final: 0.8962 (tpp) REVERT: C 378 LYS cc_start: 0.9523 (mmmt) cc_final: 0.9303 (mmmt) REVERT: C 441 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6691 (tt) REVERT: C 532 ASN cc_start: 0.9042 (t0) cc_final: 0.8594 (p0) REVERT: C 756 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7471 (t80) REVERT: C 816 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7837 (m) REVERT: C 973 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8202 (tp) outliers start: 94 outliers final: 80 residues processed: 227 average time/residue: 0.3354 time to fit residues: 127.9759 Evaluate side-chains 226 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 136 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 165 optimal weight: 0.0970 chunk 290 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.089239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062014 restraints weight = 96119.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064619 restraints weight = 56128.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065525 restraints weight = 32496.259| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26447 Z= 0.137 Angle : 0.696 15.194 36109 Z= 0.330 Chirality : 0.048 0.618 4220 Planarity : 0.005 0.078 4554 Dihedral : 7.172 101.986 4653 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 3.53 % Allowed : 26.31 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3159 helix: 1.26 (0.20), residues: 715 sheet: -0.87 (0.20), residues: 643 loop : -1.87 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.008 0.001 HIS C 339 PHE 0.025 0.001 PHE B 92 TYR 0.025 0.001 TYR C 170 ARG 0.006 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 44) link_NAG-ASN : angle 4.09213 ( 132) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 2.17751 ( 45) hydrogen bonds : bond 0.03772 ( 887) hydrogen bonds : angle 5.06748 ( 2466) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.44536 ( 76) covalent geometry : bond 0.00314 (26349) covalent geometry : angle 0.64493 (35856) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6807.68 seconds wall clock time: 121 minutes 18.53 seconds (7278.53 seconds total)