Starting phenix.real_space_refine on Mon Aug 25 06:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.map" model { file = "/net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x55_38063/08_2025/8x55_38063.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.063 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 114 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.32, per 1000 atoms: 0.25 Number of scatterers: 25749 At special positions: 0 Unit cell: (146.64, 140.4, 170.56, 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=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 282 " " 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 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 75 helices and 54 sheets defined 26.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 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: 3.713A 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 403 through 410 removed outlier: 3.804A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.692A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.350A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.577A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.271A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.646A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (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 removed outlier: 3.620A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.119A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.589A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.757A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.538A pdb=" N VAL B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.583A 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 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.528A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.508A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (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 912 through 919 removed outlier: 4.380A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.798A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.567A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.536A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.826A 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: 3.738A 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 616 through 626 removed outlier: 3.673A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.672A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.190A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.550A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.322A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.662A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.261A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.549A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1139 through 1144' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.177A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (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: 3.650A 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: 3.625A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.157A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.653A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.873A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.962A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.831A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.332A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.184A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.332A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.708A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.156A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.582A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.873A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.118A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.041A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.542A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.750A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 451 through 454 removed outlier: 3.945A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.916A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.847A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.612A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.361A 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: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.701A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.204A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.554A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.148A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.729A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.787A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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: 3.862A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.372A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.215A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.726A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 913 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 2.63 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: 8116 1.34 - 1.47: 6730 1.47 - 1.59: 11360 1.59 - 1.72: 2 1.72 - 1.85: 141 Bond restraints: 26349 Sorted by residual: bond pdb=" CG PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.503 1.215 0.288 3.40e-02 8.65e+02 7.15e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CB PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CA THR A 430 " pdb=" CB THR A 430 " ideal model delta sigma weight residual 1.526 1.567 -0.041 1.53e-02 4.27e+03 7.21e+00 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 35570 3.63 - 7.26: 268 7.26 - 10.89: 14 10.89 - 14.52: 1 14.52 - 18.15: 3 Bond angle restraints: 35856 Sorted by residual: angle pdb=" CA PRO A 209 " pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 112.00 93.85 18.15 1.40e+00 5.10e-01 1.68e+02 angle pdb=" N PRO A 209 " pdb=" CD PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 103.20 88.35 14.85 1.50e+00 4.44e-01 9.81e+01 angle pdb=" C ASN B1074 " pdb=" N PHE B1075 " pdb=" CA PHE B1075 " ideal model delta sigma weight residual 122.44 115.35 7.09 1.19e+00 7.06e-01 3.55e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 122.44 115.39 7.05 1.19e+00 7.06e-01 3.51e+01 angle pdb=" CA PRO A 463 " pdb=" N PRO A 463 " pdb=" CD PRO A 463 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 3.00e+01 ... (remaining 35851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 14640 23.03 - 46.05: 1400 46.05 - 69.08: 178 69.08 - 92.11: 122 92.11 - 115.13: 106 Dihedral angle restraints: 16446 sinusoidal: 7170 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 7.99 85.01 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 23.16 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 16443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4184 0.174 - 0.349: 34 0.349 - 0.523: 0 0.523 - 0.697: 0 0.697 - 0.872: 3 Chirality restraints: 4221 Sorted by residual: 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 -1.53 -0.87 2.00e-01 2.50e+01 1.90e+01 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 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+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 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 4218 not shown) Planarity restraints: 4599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.151 5.00e-02 4.00e+02 2.05e-01 6.74e+01 pdb=" N PRO A 209 " -0.353 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.076 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 463 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO A 82 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.048 5.00e-02 4.00e+02 ... (remaining 4596 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 451 2.64 - 3.21: 24084 3.21 - 3.77: 38977 3.77 - 4.34: 53693 4.34 - 4.90: 87066 Nonbonded interactions: 204271 Sorted by model distance: nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.075 3.040 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.120 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.166 3.120 ... (remaining 204266 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: 0.03 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: 2.290 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.730 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.005 0.288 26448 Z= 0.214 Angle : 0.853 18.148 36114 Z= 0.430 Chirality : 0.056 0.872 4221 Planarity : 0.007 0.205 4554 Dihedral : 20.861 115.132 10371 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 0.40 % Allowed : 27.06 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.15), residues: 3159 helix: 0.70 (0.20), residues: 690 sheet: -0.98 (0.20), residues: 696 loop : -1.80 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1019 TYR 0.022 0.001 TYR A 904 PHE 0.037 0.002 PHE B 135 TRP 0.048 0.003 TRP B 633 HIS 0.007 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00480 (26349) covalent geometry : angle 0.81555 (35856) SS BOND : bond 0.00554 ( 39) SS BOND : angle 2.07987 ( 78) hydrogen bonds : bond 0.20178 ( 913) hydrogen bonds : angle 8.20371 ( 2481) link_BETA1-4 : bond 0.00448 ( 15) link_BETA1-4 : angle 2.34911 ( 45) link_NAG-ASN : bond 0.00577 ( 45) link_NAG-ASN : angle 3.68017 ( 135) *********************** 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 214 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 THR cc_start: 0.9071 (m) cc_final: 0.8854 (p) REVERT: B 127 PHE cc_start: 0.8200 (t80) cc_final: 0.7835 (t80) REVERT: B 699 LEU cc_start: 0.8269 (mp) cc_final: 0.7997 (mp) REVERT: C 508 TYR cc_start: 0.8148 (m-80) cc_final: 0.7624 (m-10) outliers start: 11 outliers final: 9 residues processed: 210 average time/residue: 0.1539 time to fit residues: 53.1199 Evaluate side-chains 186 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.0170 overall best weight: 2.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1002 GLN B 774 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1064 HIS ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073106 restraints weight = 76160.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075720 restraints weight = 40904.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077448 restraints weight = 27706.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078566 restraints weight = 21499.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079320 restraints weight = 18397.482| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26448 Z= 0.179 Angle : 0.760 14.170 36114 Z= 0.366 Chirality : 0.051 0.617 4221 Planarity : 0.005 0.117 4554 Dihedral : 14.262 107.768 4668 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.34 % Favored : 92.53 % Rotamer: Outliers : 4.36 % Allowed : 22.92 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.15), residues: 3159 helix: 1.09 (0.20), residues: 690 sheet: -0.80 (0.20), residues: 669 loop : -1.78 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1019 TYR 0.023 0.002 TYR B1067 PHE 0.051 0.002 PHE C 135 TRP 0.019 0.002 TRP B 633 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00414 (26349) covalent geometry : angle 0.71514 (35856) SS BOND : bond 0.00567 ( 39) SS BOND : angle 1.56470 ( 78) hydrogen bonds : bond 0.04400 ( 913) hydrogen bonds : angle 6.18247 ( 2481) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 3.28515 ( 45) link_NAG-ASN : bond 0.00544 ( 45) link_NAG-ASN : angle 3.68050 ( 135) *********************** 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 309 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 188 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8449 (tp) cc_final: 0.8107 (tp) REVERT: A 732 THR cc_start: 0.9079 (m) cc_final: 0.8864 (p) REVERT: A 902 MET cc_start: 0.9205 (tpp) cc_final: 0.8944 (tpp) REVERT: B 127 PHE cc_start: 0.8228 (t80) cc_final: 0.7905 (m-80) REVERT: B 480 CYS cc_start: -0.0491 (OUTLIER) cc_final: -0.1678 (p) REVERT: B 508 TYR cc_start: 0.8202 (m-10) cc_final: 0.7904 (m-10) REVERT: B 699 LEU cc_start: 0.8385 (mp) cc_final: 0.8184 (mp) REVERT: B 900 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8241 (mtm) REVERT: B 926 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: C 101 ILE cc_start: 0.9344 (mm) cc_final: 0.8889 (tp) REVERT: C 191 GLU cc_start: 0.7876 (mp0) cc_final: 0.7654 (mp0) REVERT: C 578 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (t0) REVERT: C 633 TRP cc_start: 0.7788 (p90) cc_final: 0.7496 (p90) REVERT: C 1002 GLN cc_start: 0.8458 (tt0) cc_final: 0.8053 (tt0) outliers start: 121 outliers final: 68 residues processed: 290 average time/residue: 0.1285 time to fit residues: 63.8336 Evaluate side-chains 241 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 174 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN B1002 GLN B1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069669 restraints weight = 76809.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072237 restraints weight = 41372.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073927 restraints weight = 28142.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075041 restraints weight = 21891.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075761 restraints weight = 18669.639| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26448 Z= 0.211 Angle : 0.773 19.390 36114 Z= 0.371 Chirality : 0.052 0.624 4221 Planarity : 0.005 0.066 4554 Dihedral : 9.806 106.538 4659 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.62 % Rotamer: Outliers : 5.55 % Allowed : 21.98 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 3159 helix: 1.04 (0.20), residues: 693 sheet: -0.90 (0.20), residues: 660 loop : -1.80 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 346 TYR 0.022 0.002 TYR A1067 PHE 0.028 0.002 PHE C 220 TRP 0.038 0.002 TRP B 633 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00485 (26349) covalent geometry : angle 0.71722 (35856) SS BOND : bond 0.00625 ( 39) SS BOND : angle 1.63107 ( 78) hydrogen bonds : bond 0.04602 ( 913) hydrogen bonds : angle 5.79915 ( 2481) link_BETA1-4 : bond 0.00232 ( 15) link_BETA1-4 : angle 3.20189 ( 45) link_NAG-ASN : bond 0.00578 ( 45) link_NAG-ASN : angle 4.29772 ( 135) *********************** 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 341 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 187 time to evaluate : 0.994 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 173 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6656 (tm-30) REVERT: A 353 TRP cc_start: 0.7862 (p-90) cc_final: 0.7639 (p-90) REVERT: A 389 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.6648 (t70) REVERT: A 402 ILE cc_start: 0.8431 (tp) cc_final: 0.7906 (tp) REVERT: A 740 MET cc_start: 0.8184 (ttm) cc_final: 0.6610 (ttm) REVERT: A 773 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 902 MET cc_start: 0.9208 (tpp) cc_final: 0.8970 (tpp) REVERT: B 127 PHE cc_start: 0.8235 (t80) cc_final: 0.7994 (m-80) REVERT: B 389 ASP cc_start: 0.7867 (m-30) cc_final: 0.6740 (t0) REVERT: B 480 CYS cc_start: -0.0622 (OUTLIER) cc_final: -0.1633 (p) REVERT: B 495 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5726 (m-10) REVERT: B 508 TYR cc_start: 0.8526 (m-10) cc_final: 0.8222 (m-10) REVERT: B 552 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8110 (pp) REVERT: B 699 LEU cc_start: 0.8318 (mp) cc_final: 0.7992 (mt) REVERT: B 900 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8274 (mtm) REVERT: B 922 LEU cc_start: 0.8850 (mt) cc_final: 0.8641 (mp) REVERT: B 926 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: B 994 ASP cc_start: 0.8399 (t70) cc_final: 0.8167 (t70) REVERT: C 191 GLU cc_start: 0.8069 (mp0) cc_final: 0.7437 (mp0) REVERT: C 264 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.6802 (p0) REVERT: C 306 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: C 699 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7530 (mp) REVERT: C 779 GLN cc_start: 0.8944 (tp40) cc_final: 0.8597 (tm-30) REVERT: C 1002 GLN cc_start: 0.8499 (tt0) cc_final: 0.8068 (tt0) outliers start: 154 outliers final: 89 residues processed: 316 average time/residue: 0.1297 time to fit residues: 71.1254 Evaluate side-chains 265 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 167 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 39 optimal weight: 0.0870 chunk 260 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069499 restraints weight = 76349.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072131 restraints weight = 40530.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073856 restraints weight = 27252.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.074974 restraints weight = 21130.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075695 restraints weight = 17912.494| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26448 Z= 0.179 Angle : 0.724 18.345 36114 Z= 0.348 Chirality : 0.049 0.589 4221 Planarity : 0.005 0.065 4554 Dihedral : 8.675 102.384 4655 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.66 % Favored : 92.24 % Rotamer: Outliers : 5.48 % Allowed : 21.98 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 3159 helix: 1.16 (0.20), residues: 690 sheet: -0.91 (0.20), residues: 657 loop : -1.78 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE B 133 TRP 0.029 0.002 TRP B 633 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00412 (26349) covalent geometry : angle 0.66396 (35856) SS BOND : bond 0.00630 ( 39) SS BOND : angle 1.57413 ( 78) hydrogen bonds : bond 0.04199 ( 913) hydrogen bonds : angle 5.63368 ( 2481) link_BETA1-4 : bond 0.00209 ( 15) link_BETA1-4 : angle 2.98996 ( 45) link_NAG-ASN : bond 0.00637 ( 45) link_NAG-ASN : angle 4.33403 ( 135) *********************** 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 331 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 179 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7878 (p-90) cc_final: 0.7658 (p-90) REVERT: A 389 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.6747 (t70) REVERT: A 402 ILE cc_start: 0.8395 (tp) cc_final: 0.7767 (tp) REVERT: A 732 THR cc_start: 0.9229 (m) cc_final: 0.8994 (p) REVERT: A 740 MET cc_start: 0.8374 (ttm) cc_final: 0.7921 (ttm) REVERT: A 902 MET cc_start: 0.9199 (tpp) cc_final: 0.8921 (tpp) REVERT: B 127 PHE cc_start: 0.8280 (t80) cc_final: 0.8066 (m-80) REVERT: B 389 ASP cc_start: 0.7948 (m-30) cc_final: 0.6785 (t0) REVERT: B 480 CYS cc_start: -0.0756 (OUTLIER) cc_final: -0.1669 (p) REVERT: B 489 TYR cc_start: 0.7506 (m-80) cc_final: 0.7192 (m-10) REVERT: B 495 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: B 508 TYR cc_start: 0.8597 (m-10) cc_final: 0.8307 (m-10) REVERT: B 552 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 592 PHE cc_start: 0.7098 (t80) cc_final: 0.6657 (t80) REVERT: B 900 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8258 (mtm) REVERT: B 926 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: B 994 ASP cc_start: 0.8384 (t70) cc_final: 0.8167 (t70) REVERT: C 177 MET cc_start: 0.7227 (tpp) cc_final: 0.6967 (tpp) REVERT: C 191 GLU cc_start: 0.8018 (mp0) cc_final: 0.7388 (mp0) REVERT: C 264 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6431 (p0) REVERT: C 306 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: C 699 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7616 (mp) REVERT: C 779 GLN cc_start: 0.8892 (tp40) cc_final: 0.8598 (tm-30) REVERT: C 1002 GLN cc_start: 0.8520 (tt0) cc_final: 0.7956 (tt0) outliers start: 152 outliers final: 91 residues processed: 308 average time/residue: 0.1312 time to fit residues: 69.0170 Evaluate side-chains 271 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 171 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 257 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 299 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 856 ASN A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071071 restraints weight = 76243.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073711 restraints weight = 40892.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075442 restraints weight = 27622.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076564 restraints weight = 21488.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077301 restraints weight = 18238.254| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26448 Z= 0.119 Angle : 0.692 16.808 36114 Z= 0.329 Chirality : 0.049 0.581 4221 Planarity : 0.004 0.062 4554 Dihedral : 7.964 99.115 4655 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 4.00 % Allowed : 24.11 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.15), residues: 3159 helix: 1.33 (0.20), residues: 702 sheet: -0.97 (0.20), residues: 690 loop : -1.66 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.016 0.001 TYR B 837 PHE 0.025 0.001 PHE C 220 TRP 0.035 0.002 TRP B 633 HIS 0.004 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00268 (26349) covalent geometry : angle 0.63488 (35856) SS BOND : bond 0.00629 ( 39) SS BOND : angle 1.43749 ( 78) hydrogen bonds : bond 0.03801 ( 913) hydrogen bonds : angle 5.33310 ( 2481) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 2.51725 ( 45) link_NAG-ASN : bond 0.00585 ( 45) link_NAG-ASN : angle 4.22493 ( 135) *********************** 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 302 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 191 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.6729 (p0) REVERT: A 402 ILE cc_start: 0.8416 (tp) cc_final: 0.7824 (tp) REVERT: A 732 THR cc_start: 0.9158 (m) cc_final: 0.8916 (p) REVERT: A 740 MET cc_start: 0.8265 (ttm) cc_final: 0.7251 (ttm) REVERT: A 902 MET cc_start: 0.9168 (tpp) cc_final: 0.8892 (tpp) REVERT: A 1002 GLN cc_start: 0.8463 (tt0) cc_final: 0.8190 (tt0) REVERT: B 127 PHE cc_start: 0.8351 (t80) cc_final: 0.8082 (m-80) REVERT: B 389 ASP cc_start: 0.7895 (m-30) cc_final: 0.6750 (t0) REVERT: B 480 CYS cc_start: -0.0711 (OUTLIER) cc_final: -0.1612 (p) REVERT: B 508 TYR cc_start: 0.8564 (m-10) cc_final: 0.8275 (m-10) REVERT: B 588 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 592 PHE cc_start: 0.7004 (t80) cc_final: 0.6562 (t80) REVERT: B 926 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: B 994 ASP cc_start: 0.8348 (t70) cc_final: 0.8125 (t70) REVERT: C 177 MET cc_start: 0.7416 (tpp) cc_final: 0.7213 (tpp) REVERT: C 191 GLU cc_start: 0.7837 (mp0) cc_final: 0.7290 (mp0) REVERT: C 264 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6341 (p0) REVERT: C 386 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7649 (ptpp) REVERT: C 508 TYR cc_start: 0.8622 (m-10) cc_final: 0.8125 (m-80) REVERT: C 1002 GLN cc_start: 0.8474 (tt0) cc_final: 0.7905 (tt0) outliers start: 111 outliers final: 71 residues processed: 280 average time/residue: 0.1341 time to fit residues: 64.7835 Evaluate side-chains 247 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 171 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 542 ASN A 628 GLN A 804 GLN A1011 GLN B 955 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 542 ASN C 628 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.095229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066294 restraints weight = 77177.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068749 restraints weight = 42300.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070372 restraints weight = 29114.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071419 restraints weight = 22901.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072118 restraints weight = 19616.505| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26448 Z= 0.274 Angle : 0.787 16.105 36114 Z= 0.383 Chirality : 0.051 0.589 4221 Planarity : 0.005 0.059 4554 Dihedral : 8.146 98.025 4655 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.52 % Rotamer: Outliers : 5.91 % Allowed : 22.56 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.15), residues: 3159 helix: 1.12 (0.20), residues: 702 sheet: -1.09 (0.19), residues: 714 loop : -1.77 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.022 0.002 TYR A1067 PHE 0.027 0.002 PHE B 592 TRP 0.036 0.002 TRP B 633 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00632 (26349) covalent geometry : angle 0.73416 (35856) SS BOND : bond 0.00687 ( 39) SS BOND : angle 1.87809 ( 78) hydrogen bonds : bond 0.04623 ( 913) hydrogen bonds : angle 5.64038 ( 2481) link_BETA1-4 : bond 0.00211 ( 15) link_BETA1-4 : angle 2.36350 ( 45) link_NAG-ASN : bond 0.00632 ( 45) link_NAG-ASN : angle 4.32121 ( 135) *********************** 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 332 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 168 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7154 (p0) REVERT: A 389 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.6766 (t70) REVERT: A 698 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8043 (p) REVERT: A 759 PHE cc_start: 0.7822 (m-10) cc_final: 0.7012 (m-10) REVERT: A 784 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: B 23 THR cc_start: 0.4545 (m) cc_final: 0.4218 (m) REVERT: B 101 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9047 (tp) REVERT: B 306 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8751 (m-10) REVERT: B 389 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.6887 (t0) REVERT: B 480 CYS cc_start: -0.0876 (OUTLIER) cc_final: -0.1668 (p) REVERT: B 489 TYR cc_start: 0.7478 (m-80) cc_final: 0.7234 (m-10) REVERT: B 508 TYR cc_start: 0.8792 (m-10) cc_final: 0.8508 (m-10) REVERT: B 779 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8595 (tt0) REVERT: B 900 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: B 926 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: B 994 ASP cc_start: 0.8486 (t70) cc_final: 0.8256 (t70) REVERT: C 191 GLU cc_start: 0.8209 (mp0) cc_final: 0.8005 (mp0) REVERT: C 264 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.6752 (p0) REVERT: C 306 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: C 386 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7845 (ptpp) REVERT: C 508 TYR cc_start: 0.8749 (m-10) cc_final: 0.8438 (m-10) REVERT: C 578 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8581 (t0) REVERT: C 699 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7892 (mp) REVERT: C 856 ASN cc_start: 0.8610 (t0) cc_final: 0.8402 (t0) REVERT: C 1002 GLN cc_start: 0.8586 (tt0) cc_final: 0.7949 (tt0) outliers start: 164 outliers final: 106 residues processed: 310 average time/residue: 0.1403 time to fit residues: 75.3579 Evaluate side-chains 274 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 154 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 230 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.094792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066216 restraints weight = 76858.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068668 restraints weight = 41769.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070294 restraints weight = 28627.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071345 restraints weight = 22434.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072008 restraints weight = 19145.335| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26448 Z= 0.232 Angle : 0.751 15.402 36114 Z= 0.363 Chirality : 0.050 0.592 4221 Planarity : 0.005 0.060 4554 Dihedral : 8.086 99.103 4655 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.66 % Favored : 92.24 % Rotamer: Outliers : 5.05 % Allowed : 24.18 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 699 sheet: -1.17 (0.19), residues: 684 loop : -1.74 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.019 0.002 TYR A1067 PHE 0.029 0.002 PHE A 220 TRP 0.045 0.002 TRP B 633 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00536 (26349) covalent geometry : angle 0.69795 (35856) SS BOND : bond 0.00561 ( 39) SS BOND : angle 1.59213 ( 78) hydrogen bonds : bond 0.04360 ( 913) hydrogen bonds : angle 5.57037 ( 2481) link_BETA1-4 : bond 0.00235 ( 15) link_BETA1-4 : angle 2.20281 ( 45) link_NAG-ASN : bond 0.00595 ( 45) link_NAG-ASN : angle 4.27638 ( 135) *********************** 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 296 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 156 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7421 (ptmt) REVERT: A 264 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7372 (p0) REVERT: A 386 LYS cc_start: 0.8450 (mtmm) cc_final: 0.7912 (ptpt) REVERT: A 389 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.6716 (t0) REVERT: A 402 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 633 TRP cc_start: 0.8136 (p90) cc_final: 0.7812 (p90) REVERT: A 698 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 784 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: B 23 THR cc_start: 0.4542 (m) cc_final: 0.4144 (m) REVERT: B 101 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9067 (tp) REVERT: B 306 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: B 335 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 389 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.6964 (t0) REVERT: B 480 CYS cc_start: -0.0807 (OUTLIER) cc_final: -0.1581 (p) REVERT: B 489 TYR cc_start: 0.7486 (m-80) cc_final: 0.7232 (m-10) REVERT: B 508 TYR cc_start: 0.8830 (m-10) cc_final: 0.8590 (m-10) REVERT: B 900 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8148 (mtm) REVERT: B 926 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: B 994 ASP cc_start: 0.8521 (t70) cc_final: 0.8304 (t70) REVERT: C 191 GLU cc_start: 0.8178 (mp0) cc_final: 0.7611 (mp0) REVERT: C 264 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.6764 (p0) REVERT: C 386 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8026 (ptpt) REVERT: C 508 TYR cc_start: 0.8797 (m-10) cc_final: 0.8432 (m-80) REVERT: C 699 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7926 (mp) outliers start: 140 outliers final: 107 residues processed: 274 average time/residue: 0.1394 time to fit residues: 65.5509 Evaluate side-chains 267 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 145 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 307 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 200 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.095612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067241 restraints weight = 76785.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069744 restraints weight = 41502.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071410 restraints weight = 28239.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072444 restraints weight = 22030.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073166 restraints weight = 18821.171| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26448 Z= 0.156 Angle : 0.709 15.135 36114 Z= 0.340 Chirality : 0.049 0.580 4221 Planarity : 0.004 0.057 4554 Dihedral : 7.891 97.461 4655 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.66 % Favored : 92.24 % Rotamer: Outliers : 4.40 % Allowed : 25.26 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.15), residues: 3159 helix: 1.38 (0.20), residues: 699 sheet: -1.14 (0.19), residues: 699 loop : -1.69 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.016 0.001 TYR A1067 PHE 0.030 0.001 PHE A 220 TRP 0.043 0.002 TRP B 633 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00362 (26349) covalent geometry : angle 0.65775 (35856) SS BOND : bond 0.00498 ( 39) SS BOND : angle 1.44715 ( 78) hydrogen bonds : bond 0.04047 ( 913) hydrogen bonds : angle 5.38130 ( 2481) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 2.06021 ( 45) link_NAG-ASN : bond 0.00581 ( 45) link_NAG-ASN : angle 4.13738 ( 135) *********************** 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 287 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 165 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7205 (p0) REVERT: A 353 TRP cc_start: 0.8146 (p-90) cc_final: 0.7738 (p-90) REVERT: A 386 LYS cc_start: 0.8409 (mtmm) cc_final: 0.7924 (ptpt) REVERT: A 389 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.6817 (t0) REVERT: A 402 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 698 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 784 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: A 902 MET cc_start: 0.9226 (tpp) cc_final: 0.8927 (tpp) REVERT: B 23 THR cc_start: 0.4409 (m) cc_final: 0.3992 (m) REVERT: B 101 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9155 (tp) REVERT: B 118 LEU cc_start: 0.9026 (tp) cc_final: 0.8691 (tp) REVERT: B 119 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8863 (mp) REVERT: B 306 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8428 (m-10) REVERT: B 335 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (tt) REVERT: B 480 CYS cc_start: -0.0601 (OUTLIER) cc_final: -0.1267 (p) REVERT: B 489 TYR cc_start: 0.7467 (m-80) cc_final: 0.7218 (m-10) REVERT: B 508 TYR cc_start: 0.8797 (m-10) cc_final: 0.8579 (m-10) REVERT: B 779 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8558 (tt0) REVERT: B 841 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.4582 (mp) REVERT: B 926 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: B 994 ASP cc_start: 0.8479 (t70) cc_final: 0.8258 (t70) REVERT: C 191 GLU cc_start: 0.8020 (mp0) cc_final: 0.7367 (mp0) REVERT: C 264 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.6793 (p0) REVERT: C 386 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7942 (ptpt) REVERT: C 508 TYR cc_start: 0.8733 (m-10) cc_final: 0.8496 (m-10) REVERT: C 699 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7834 (mp) REVERT: C 990 GLU cc_start: 0.7886 (pm20) cc_final: 0.7469 (pm20) REVERT: C 1002 GLN cc_start: 0.8444 (tt0) cc_final: 0.8120 (tt0) outliers start: 122 outliers final: 95 residues processed: 268 average time/residue: 0.1373 time to fit residues: 62.7288 Evaluate side-chains 258 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 149 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 43 optimal weight: 0.0020 chunk 119 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.3691 r_free = 0.3691 target = 0.095718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067458 restraints weight = 77051.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069955 restraints weight = 41393.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071604 restraints weight = 28130.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072690 restraints weight = 21928.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073391 restraints weight = 18634.169| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26448 Z= 0.157 Angle : 0.708 14.841 36114 Z= 0.339 Chirality : 0.049 0.582 4221 Planarity : 0.004 0.056 4554 Dihedral : 7.790 96.568 4655 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.72 % Favored : 92.18 % Rotamer: Outliers : 4.47 % Allowed : 25.26 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.15), residues: 3159 helix: 1.44 (0.20), residues: 699 sheet: -1.13 (0.19), residues: 705 loop : -1.65 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.016 0.001 TYR A1067 PHE 0.040 0.001 PHE A 220 TRP 0.045 0.002 TRP B 633 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00365 (26349) covalent geometry : angle 0.65707 (35856) SS BOND : bond 0.00488 ( 39) SS BOND : angle 1.43759 ( 78) hydrogen bonds : bond 0.03971 ( 913) hydrogen bonds : angle 5.32685 ( 2481) link_BETA1-4 : bond 0.00303 ( 15) link_BETA1-4 : angle 2.02499 ( 45) link_NAG-ASN : bond 0.00570 ( 45) link_NAG-ASN : angle 4.09127 ( 135) *********************** 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 281 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 157 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7417 (p0) REVERT: A 353 TRP cc_start: 0.8151 (p-90) cc_final: 0.7674 (p-90) REVERT: A 386 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7877 (ptpt) REVERT: A 389 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.6814 (t0) REVERT: A 402 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 698 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8115 (p) REVERT: A 784 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: A 902 MET cc_start: 0.9203 (tpp) cc_final: 0.8915 (tpp) REVERT: B 101 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9146 (tp) REVERT: B 119 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8860 (mp) REVERT: B 306 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: B 335 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 480 CYS cc_start: -0.0618 (OUTLIER) cc_final: -0.1256 (p) REVERT: B 489 TYR cc_start: 0.7426 (m-80) cc_final: 0.7179 (m-10) REVERT: B 508 TYR cc_start: 0.8818 (m-10) cc_final: 0.8575 (m-10) REVERT: B 592 PHE cc_start: 0.7150 (t80) cc_final: 0.6877 (t80) REVERT: B 779 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8567 (tt0) REVERT: B 900 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: B 926 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: B 994 ASP cc_start: 0.8465 (t70) cc_final: 0.8243 (t70) REVERT: C 191 GLU cc_start: 0.8015 (mp0) cc_final: 0.7431 (mp0) REVERT: C 264 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.6827 (p0) REVERT: C 386 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7769 (ptpt) REVERT: C 508 TYR cc_start: 0.8743 (m-10) cc_final: 0.8475 (m-80) REVERT: C 699 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7805 (mp) REVERT: C 990 GLU cc_start: 0.7856 (pm20) cc_final: 0.7435 (pm20) REVERT: C 1002 GLN cc_start: 0.8548 (tt0) cc_final: 0.8084 (tt0) outliers start: 124 outliers final: 97 residues processed: 263 average time/residue: 0.1387 time to fit residues: 62.9272 Evaluate side-chains 263 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 152 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 139 optimal weight: 0.5980 chunk 267 optimal weight: 0.9980 chunk 283 optimal weight: 0.0050 chunk 159 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069063 restraints weight = 76596.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071621 restraints weight = 40908.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073335 restraints weight = 27682.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074397 restraints weight = 21445.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075137 restraints weight = 18237.964| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26448 Z= 0.116 Angle : 0.691 14.670 36114 Z= 0.329 Chirality : 0.049 0.577 4221 Planarity : 0.004 0.056 4554 Dihedral : 7.523 94.652 4655 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 3.39 % Allowed : 26.05 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3159 helix: 1.51 (0.20), residues: 705 sheet: -1.08 (0.19), residues: 699 loop : -1.53 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.016 0.001 TYR B 501 PHE 0.026 0.001 PHE A 220 TRP 0.044 0.002 TRP C 633 HIS 0.002 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00262 (26349) covalent geometry : angle 0.64050 (35856) SS BOND : bond 0.00455 ( 39) SS BOND : angle 1.48681 ( 78) hydrogen bonds : bond 0.03663 ( 913) hydrogen bonds : angle 5.13260 ( 2481) link_BETA1-4 : bond 0.00465 ( 15) link_BETA1-4 : angle 1.97834 ( 45) link_NAG-ASN : bond 0.00591 ( 45) link_NAG-ASN : angle 4.00420 ( 135) ********************** 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 261 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 167 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.8178 (m-10) cc_final: 0.7779 (m-10) REVERT: A 177 MET cc_start: 0.7282 (tpp) cc_final: 0.5859 (mmt) REVERT: A 191 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7399 (mp0) REVERT: A 264 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 353 TRP cc_start: 0.8042 (p-90) cc_final: 0.7751 (p-90) REVERT: A 386 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7940 (ptpt) REVERT: A 402 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 698 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8113 (p) REVERT: A 902 MET cc_start: 0.9175 (tpp) cc_final: 0.8880 (tpp) REVERT: B 335 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 480 CYS cc_start: -0.0637 (OUTLIER) cc_final: -0.1239 (p) REVERT: B 489 TYR cc_start: 0.7370 (m-80) cc_final: 0.7120 (m-10) REVERT: B 508 TYR cc_start: 0.8734 (m-10) cc_final: 0.8474 (m-10) REVERT: B 592 PHE cc_start: 0.7174 (t80) cc_final: 0.6896 (t80) REVERT: B 779 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8533 (tt0) REVERT: B 926 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: B 994 ASP cc_start: 0.8403 (t70) cc_final: 0.8200 (t70) REVERT: C 177 MET cc_start: 0.7183 (tpp) cc_final: 0.6109 (mmt) REVERT: C 264 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7590 (p0) REVERT: C 306 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: C 386 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7928 (ptpt) REVERT: C 699 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 990 GLU cc_start: 0.7817 (pm20) cc_final: 0.7416 (pm20) REVERT: C 1002 GLN cc_start: 0.8466 (tt0) cc_final: 0.8043 (tt0) outliers start: 94 outliers final: 73 residues processed: 243 average time/residue: 0.1364 time to fit residues: 56.5230 Evaluate side-chains 233 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 151 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 57 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 0.0370 chunk 214 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068837 restraints weight = 76265.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071368 restraints weight = 40919.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073059 restraints weight = 27747.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074103 restraints weight = 21576.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074851 restraints weight = 18369.023| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26448 Z= 0.126 Angle : 0.687 14.407 36114 Z= 0.327 Chirality : 0.049 0.571 4221 Planarity : 0.004 0.056 4554 Dihedral : 7.464 92.202 4655 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 3.28 % Allowed : 26.41 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3159 helix: 1.51 (0.20), residues: 705 sheet: -1.01 (0.19), residues: 720 loop : -1.55 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.022 0.001 TYR C 508 PHE 0.028 0.001 PHE C 175 TRP 0.045 0.002 TRP C 633 HIS 0.004 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00292 (26349) covalent geometry : angle 0.63708 (35856) SS BOND : bond 0.00436 ( 39) SS BOND : angle 1.42731 ( 78) hydrogen bonds : bond 0.03691 ( 913) hydrogen bonds : angle 5.08959 ( 2481) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.97149 ( 45) link_NAG-ASN : bond 0.00592 ( 45) link_NAG-ASN : angle 3.99716 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.48 seconds wall clock time: 70 minutes 1.30 seconds (4201.30 seconds total)