Starting phenix.real_space_refine on Sun Oct 12 16:59:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.map" model { file = "/net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x56_38064/10_2025/8x56_38064.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16422 2.51 5 N 4197 2.21 5 O 5016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/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: 5.46, per 1000 atoms: 0.21 Number of scatterers: 25749 At special positions: 0 Unit cell: (143.52, 142.48, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5016 8.00 N 4197 7.00 C 16422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 331 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 282 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 998.2 milliseconds Enol-peptide restraints added in 476.8 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: 67 helices and 53 sheets defined 25.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.647A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.968A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.858A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.703A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.790A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.594A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.855A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.991A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.550A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.876A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.598A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.829A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.361A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.623A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.510A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.050A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.620A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.649A pdb=" N VAL C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 618 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.408A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.581A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.436A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.742A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.502A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.277A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.621A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.172A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.764A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.038A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.932A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.914A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.863A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.629A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.811A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.844A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.207A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.198A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.586A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.577A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.999A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.698A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.311A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.239A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.847A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.951A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.964A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.590A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.548A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.601A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.378A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.527A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.520A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.081A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.507A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.542A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.589A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.104A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.542A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.638A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.608A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.814A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 891 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8118 1.34 - 1.47: 6745 1.47 - 1.60: 11345 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 26349 Sorted by residual: bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.30e+01 bond pdb=" N ILE C 212 " pdb=" CA ILE C 212 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" N ILE C 210 " pdb=" CA ILE C 210 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.91e+00 bond pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 1.462 1.489 -0.028 9.30e-03 1.16e+04 8.79e+00 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 34587 1.97 - 3.95: 1027 3.95 - 5.92: 186 5.92 - 7.90: 48 7.90 - 9.87: 8 Bond angle restraints: 35856 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.46 6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" N LEU B 387 " pdb=" CA LEU B 387 " pdb=" C LEU B 387 " ideal model delta sigma weight residual 114.62 108.81 5.81 1.14e+00 7.69e-01 2.60e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 115.59 6.31 1.26e+00 6.30e-01 2.50e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 112.96 108.46 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 115.89 110.37 5.52 1.32e+00 5.74e-01 1.75e+01 ... (remaining 35851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 14604 23.08 - 46.16: 1421 46.16 - 69.24: 162 69.24 - 92.32: 143 92.32 - 115.40: 113 Dihedral angle restraints: 16443 sinusoidal: 7167 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.82 83.18 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 26.01 66.99 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 33.06 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4185 0.180 - 0.360: 32 0.360 - 0.540: 0 0.540 - 0.721: 0 0.721 - 0.901: 3 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 ... (remaining 4217 not shown) Planarity restraints: 4598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO A 82 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 217 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 237 " 0.288 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG C 237 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 237 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 237 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 237 " 0.009 2.00e-02 2.50e+03 ... (remaining 4595 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 449 2.63 - 3.20: 23986 3.20 - 3.77: 40142 3.77 - 4.33: 53976 4.33 - 4.90: 87247 Nonbonded interactions: 205800 Sorted by model distance: nonbonded pdb=" OD1 ASN B 532 " pdb=" N LEU B 533 " model vdw 2.064 3.120 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.115 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" O7 NAG C1301 " model vdw 2.138 3.040 nonbonded pdb=" NE2 GLN C 173 " pdb=" O PRO C 174 " model vdw 2.138 3.120 nonbonded pdb=" O ASN B 978 " pdb=" OG1 THR C 547 " model vdw 2.148 3.040 ... (remaining 205795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.550 Find NCS groups from input model: 0.590 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26447 Z= 0.228 Angle : 0.867 18.118 36109 Z= 0.438 Chirality : 0.056 0.901 4220 Planarity : 0.006 0.129 4554 Dihedral : 21.396 115.405 10371 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.96 % Favored : 92.85 % Rotamer: Outliers : 0.58 % Allowed : 27.32 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -1.65 (0.15), residues: 3159 helix: 0.91 (0.20), residues: 699 sheet: -0.93 (0.21), residues: 584 loop : -2.04 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.023 0.001 TYR A 365 PHE 0.034 0.001 PHE C 342 TRP 0.050 0.002 TRP B 633 HIS 0.010 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00422 (26349) covalent geometry : angle 0.80896 (35856) SS BOND : bond 0.00464 ( 38) SS BOND : angle 1.71028 ( 76) hydrogen bonds : bond 0.20853 ( 887) hydrogen bonds : angle 8.35984 ( 2466) Misc. bond : bond 0.00045 ( 1) link_BETA1-4 : bond 0.00478 ( 15) link_BETA1-4 : angle 2.37167 ( 45) link_NAG-ASN : bond 0.00853 ( 44) link_NAG-ASN : angle 4.91707 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8885 (mmm) cc_final: 0.8587 (mmp) REVERT: A 896 ILE cc_start: 0.8637 (tp) cc_final: 0.8074 (tt) REVERT: A 1050 MET cc_start: 0.7898 (ptp) cc_final: 0.7558 (ptp) REVERT: A 1107 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7343 (mmt-90) REVERT: B 102 ARG cc_start: 0.4296 (ptt180) cc_final: 0.3865 (mtt180) REVERT: B 377 PHE cc_start: 0.7024 (t80) cc_final: 0.6745 (t80) REVERT: B 882 ILE cc_start: 0.9227 (pt) cc_final: 0.8853 (mt) REVERT: B 985 ASP cc_start: 0.7608 (p0) cc_final: 0.7390 (p0) REVERT: C 699 LEU cc_start: 0.8592 (mt) cc_final: 0.8367 (mp) outliers start: 16 outliers final: 8 residues processed: 184 average time/residue: 0.1544 time to fit residues: 47.7089 Evaluate side-chains 161 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 218 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.092958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067544 restraints weight = 93996.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068253 restraints weight = 64817.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068984 restraints weight = 44879.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069309 restraints weight = 41319.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069431 restraints weight = 36995.032| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26447 Z= 0.202 Angle : 0.809 17.012 36109 Z= 0.383 Chirality : 0.052 0.653 4220 Planarity : 0.005 0.071 4554 Dihedral : 14.126 108.593 4663 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 3.86 % Allowed : 23.53 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: 0.97 (0.20), residues: 714 sheet: -0.98 (0.20), residues: 613 loop : -1.94 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.028 0.002 TYR B 204 PHE 0.016 0.002 PHE C1042 TRP 0.016 0.001 TRP B 633 HIS 0.007 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00455 (26349) covalent geometry : angle 0.74289 (35856) SS BOND : bond 0.00400 ( 38) SS BOND : angle 1.61671 ( 76) hydrogen bonds : bond 0.04633 ( 887) hydrogen bonds : angle 6.21527 ( 2466) Misc. bond : bond 0.00029 ( 1) link_BETA1-4 : bond 0.00276 ( 15) link_BETA1-4 : angle 3.55677 ( 45) link_NAG-ASN : bond 0.00782 ( 44) link_NAG-ASN : angle 4.82684 ( 132) *********************** 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 261 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 154 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 127 PHE cc_start: 0.8050 (t80) cc_final: 0.7687 (t80) REVERT: A 177 MET cc_start: 0.5531 (mmt) cc_final: 0.3400 (tmm) REVERT: A 220 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.6248 (t80) REVERT: A 896 ILE cc_start: 0.8822 (tp) cc_final: 0.8296 (tt) REVERT: B 102 ARG cc_start: 0.3793 (ptt180) cc_final: 0.3456 (ptt-90) REVERT: B 164 ASN cc_start: 0.5787 (OUTLIER) cc_final: 0.5239 (p0) REVERT: B 204 TYR cc_start: 0.7380 (m-10) cc_final: 0.6899 (m-10) REVERT: B 904 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: B 909 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8925 (tp) REVERT: C 173 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6819 (tp-100) REVERT: C 726 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8500 (mm) REVERT: C 756 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7349 (t80) REVERT: C 816 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.7277 (m) outliers start: 107 outliers final: 49 residues processed: 242 average time/residue: 0.1568 time to fit residues: 63.1835 Evaluate side-chains 191 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 174 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 321 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.088703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061345 restraints weight = 96893.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063113 restraints weight = 56631.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063973 restraints weight = 36287.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064137 restraints weight = 33916.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064362 restraints weight = 29760.012| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26447 Z= 0.264 Angle : 0.818 16.376 36109 Z= 0.398 Chirality : 0.052 0.625 4220 Planarity : 0.005 0.058 4554 Dihedral : 9.306 111.749 4656 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.80 % Rotamer: Outliers : 6.16 % Allowed : 23.32 % Favored : 70.52 % 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: -1.76 (0.15), residues: 3159 helix: 0.74 (0.19), residues: 716 sheet: -1.13 (0.21), residues: 560 loop : -2.04 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 346 TYR 0.024 0.002 TYR B 204 PHE 0.027 0.002 PHE A 562 TRP 0.025 0.002 TRP C 633 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00592 (26349) covalent geometry : angle 0.75481 (35856) SS BOND : bond 0.00704 ( 38) SS BOND : angle 1.82226 ( 76) hydrogen bonds : bond 0.05016 ( 887) hydrogen bonds : angle 6.00291 ( 2466) Misc. bond : bond 0.00107 ( 1) link_BETA1-4 : bond 0.00302 ( 15) link_BETA1-4 : angle 3.38231 ( 45) link_NAG-ASN : bond 0.00799 ( 44) link_NAG-ASN : angle 4.73077 ( 132) *********************** 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 312 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 141 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 177 MET cc_start: 0.5601 (mmt) cc_final: 0.3211 (tmm) REVERT: A 188 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 220 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6487 (t80) REVERT: A 740 MET cc_start: 0.8630 (ttm) cc_final: 0.8344 (ttm) REVERT: A 896 ILE cc_start: 0.9103 (tp) cc_final: 0.8657 (tt) REVERT: A 1031 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7226 (tt0) REVERT: B 102 ARG cc_start: 0.3985 (ptt180) cc_final: 0.3693 (ptt-90) REVERT: B 164 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.5572 (p0) REVERT: B 740 MET cc_start: 0.8131 (tpp) cc_final: 0.7926 (tpt) REVERT: B 904 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: C 173 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6909 (tp-100) REVERT: C 265 TYR cc_start: 0.7302 (t80) cc_final: 0.6957 (t80) REVERT: C 378 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9271 (mmmt) REVERT: C 532 ASN cc_start: 0.9057 (t0) cc_final: 0.8684 (t0) REVERT: C 636 TYR cc_start: 0.7386 (t80) cc_final: 0.7182 (t80) REVERT: C 726 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8653 (mm) REVERT: C 756 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 759 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7313 (m-80) outliers start: 171 outliers final: 96 residues processed: 293 average time/residue: 0.1582 time to fit residues: 76.9614 Evaluate side-chains 226 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 122 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 39 optimal weight: 0.0770 chunk 260 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 147 optimal weight: 0.0070 chunk 261 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 overall best weight: 1.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 321 GLN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 437 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.090042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062431 restraints weight = 95593.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065178 restraints weight = 57077.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065966 restraints weight = 32689.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066358 restraints weight = 28023.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066480 restraints weight = 25879.153| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26447 Z= 0.146 Angle : 0.717 15.632 36109 Z= 0.343 Chirality : 0.050 0.612 4220 Planarity : 0.005 0.064 4554 Dihedral : 8.287 105.327 4656 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.12 % Favored : 92.78 % Rotamer: Outliers : 4.72 % Allowed : 24.83 % Favored : 70.45 % 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: -1.64 (0.15), residues: 3159 helix: 1.07 (0.20), residues: 711 sheet: -1.23 (0.20), residues: 632 loop : -2.01 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR B 495 PHE 0.028 0.001 PHE B 592 TRP 0.022 0.002 TRP C 104 HIS 0.005 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00330 (26349) covalent geometry : angle 0.65149 (35856) SS BOND : bond 0.00405 ( 38) SS BOND : angle 1.47426 ( 76) hydrogen bonds : bond 0.04166 ( 887) hydrogen bonds : angle 5.58154 ( 2466) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00245 ( 15) link_BETA1-4 : angle 3.00356 ( 45) link_NAG-ASN : bond 0.00763 ( 44) link_NAG-ASN : angle 4.58849 ( 132) *********************** 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 276 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 145 time to evaluate : 1.064 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 127 PHE cc_start: 0.8764 (t80) cc_final: 0.8183 (t80) REVERT: A 177 MET cc_start: 0.5690 (mmt) cc_final: 0.3907 (tmm) REVERT: A 220 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6239 (t80) REVERT: A 896 ILE cc_start: 0.9124 (tp) cc_final: 0.8794 (tt) REVERT: A 900 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8576 (pmm) REVERT: A 902 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: B 54 LEU cc_start: 0.8900 (mm) cc_final: 0.8653 (mt) REVERT: B 164 ASN cc_start: 0.6141 (OUTLIER) cc_final: 0.5674 (p0) REVERT: B 204 TYR cc_start: 0.7634 (m-10) cc_final: 0.7031 (m-10) REVERT: B 401 VAL cc_start: 0.3163 (OUTLIER) cc_final: 0.2846 (t) REVERT: B 869 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8045 (pmm) REVERT: B 1029 MET cc_start: 0.9149 (tpp) cc_final: 0.8331 (tpp) REVERT: C 265 TYR cc_start: 0.7395 (t80) cc_final: 0.6984 (t80) REVERT: C 328 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5748 (ttp80) REVERT: C 378 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9274 (mmmt) REVERT: C 532 ASN cc_start: 0.9044 (t0) cc_final: 0.8387 (p0) REVERT: C 636 TYR cc_start: 0.7349 (t80) cc_final: 0.7125 (t80) REVERT: C 726 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 756 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7476 (t80) REVERT: C 759 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: C 816 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7627 (m) outliers start: 131 outliers final: 76 residues processed: 259 average time/residue: 0.1563 time to fit residues: 68.1145 Evaluate side-chains 210 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 257 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 293 optimal weight: 0.0670 chunk 228 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 957 GLN B1119 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.091237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063711 restraints weight = 95585.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066338 restraints weight = 57325.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067198 restraints weight = 33938.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067559 restraints weight = 27236.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067676 restraints weight = 25581.853| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26447 Z= 0.118 Angle : 0.691 15.370 36109 Z= 0.330 Chirality : 0.049 0.608 4220 Planarity : 0.004 0.052 4554 Dihedral : 7.694 100.945 4655 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 4.72 % Allowed : 24.72 % 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: -1.47 (0.15), residues: 3159 helix: 1.27 (0.20), residues: 707 sheet: -0.99 (0.20), residues: 629 loop : -1.98 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.027 0.001 TYR A 369 PHE 0.022 0.001 PHE B 168 TRP 0.020 0.001 TRP C 633 HIS 0.006 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00264 (26349) covalent geometry : angle 0.62916 (35856) SS BOND : bond 0.00449 ( 38) SS BOND : angle 1.26890 ( 76) hydrogen bonds : bond 0.03818 ( 887) hydrogen bonds : angle 5.33032 ( 2466) Misc. bond : bond 0.00051 ( 1) link_BETA1-4 : bond 0.00366 ( 15) link_BETA1-4 : angle 2.61079 ( 45) link_NAG-ASN : bond 0.00749 ( 44) link_NAG-ASN : angle 4.45770 ( 132) *********************** 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 269 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 138 time to evaluate : 1.059 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 127 PHE cc_start: 0.8723 (t80) cc_final: 0.8109 (t80) REVERT: A 177 MET cc_start: 0.5730 (mmt) cc_final: 0.3888 (tmm) REVERT: A 630 THR cc_start: 0.8331 (m) cc_final: 0.8106 (p) REVERT: A 697 MET cc_start: 0.8669 (mmm) cc_final: 0.8264 (mmm) REVERT: A 896 ILE cc_start: 0.8988 (tp) cc_final: 0.8750 (tp) REVERT: B 54 LEU cc_start: 0.8875 (mm) cc_final: 0.8593 (mt) REVERT: B 164 ASN cc_start: 0.6291 (OUTLIER) cc_final: 0.5798 (p0) REVERT: B 204 TYR cc_start: 0.7496 (m-10) cc_final: 0.7016 (m-10) REVERT: B 401 VAL cc_start: 0.2679 (OUTLIER) cc_final: 0.2456 (t) REVERT: B 546 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7904 (pp) REVERT: B 563 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8281 (mm110) REVERT: B 869 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8011 (pmm) REVERT: C 328 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5863 (ttp80) REVERT: C 378 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9268 (mmmt) REVERT: C 441 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 532 ASN cc_start: 0.9054 (t0) cc_final: 0.8697 (t0) REVERT: C 697 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: C 726 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (mm) REVERT: C 756 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7447 (t80) REVERT: C 759 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: C 816 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (m) REVERT: C 973 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8159 (tp) outliers start: 131 outliers final: 79 residues processed: 251 average time/residue: 0.1536 time to fit residues: 65.2772 Evaluate side-chains 229 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 137 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 784 GLN A1108 ASN B 563 GLN B 957 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059069 restraints weight = 98134.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061121 restraints weight = 56607.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061598 restraints weight = 35751.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061897 restraints weight = 33585.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061935 restraints weight = 29706.754| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 26447 Z= 0.339 Angle : 0.856 16.772 36109 Z= 0.421 Chirality : 0.052 0.642 4220 Planarity : 0.005 0.076 4554 Dihedral : 7.948 107.160 4653 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.50 % Favored : 90.41 % Rotamer: Outliers : 5.80 % Allowed : 24.32 % Favored : 69.87 % 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: -1.79 (0.15), residues: 3159 helix: 0.75 (0.19), residues: 725 sheet: -1.17 (0.20), residues: 630 loop : -2.10 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 328 TYR 0.025 0.002 TYR B1067 PHE 0.025 0.002 PHE B 927 TRP 0.031 0.002 TRP C 633 HIS 0.012 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00764 (26349) covalent geometry : angle 0.80069 (35856) SS BOND : bond 0.00604 ( 38) SS BOND : angle 2.03607 ( 76) hydrogen bonds : bond 0.04974 ( 887) hydrogen bonds : angle 5.78467 ( 2466) Misc. bond : bond 0.00103 ( 1) link_BETA1-4 : bond 0.00366 ( 15) link_BETA1-4 : angle 2.89955 ( 45) link_NAG-ASN : bond 0.00819 ( 44) link_NAG-ASN : angle 4.58200 ( 132) *********************** 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 290 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 129 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 488 CYS cc_start: -0.3730 (OUTLIER) cc_final: -0.3956 (p) REVERT: A 495 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.3686 (m-80) REVERT: A 630 THR cc_start: 0.8297 (m) cc_final: 0.8088 (p) REVERT: A 896 ILE cc_start: 0.9109 (tp) cc_final: 0.8827 (tp) REVERT: A 1050 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7971 (ptp) REVERT: A 1107 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7578 (mmt-90) REVERT: B 54 LEU cc_start: 0.9037 (mm) cc_final: 0.8686 (mt) REVERT: B 55 PHE cc_start: 0.7730 (m-80) cc_final: 0.7397 (m-10) REVERT: B 164 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5814 (p0) REVERT: B 200 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 204 TYR cc_start: 0.7437 (m-10) cc_final: 0.6911 (m-10) REVERT: B 495 TYR cc_start: 0.0459 (OUTLIER) cc_final: -0.0662 (t80) REVERT: B 697 MET cc_start: 0.8700 (mmm) cc_final: 0.8371 (tpt) REVERT: B 869 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8101 (pmm) REVERT: C 265 TYR cc_start: 0.7496 (t80) cc_final: 0.7221 (t80) REVERT: C 328 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5795 (ttp80) REVERT: C 441 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6876 (tt) REVERT: C 532 ASN cc_start: 0.9056 (t0) cc_final: 0.8543 (p0) REVERT: C 586 ASP cc_start: 0.7731 (t0) cc_final: 0.7490 (t0) REVERT: C 726 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 756 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7712 (t80) REVERT: C 759 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: C 816 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (m) REVERT: C 1005 GLN cc_start: 0.8707 (tp40) cc_final: 0.8484 (tp40) outliers start: 161 outliers final: 116 residues processed: 269 average time/residue: 0.1539 time to fit residues: 70.4012 Evaluate side-chains 255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 125 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 230 optimal weight: 0.0770 chunk 8 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 628 GLN B 957 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.089053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061651 restraints weight = 95556.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064219 restraints weight = 58690.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064675 restraints weight = 35285.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065425 restraints weight = 29639.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065436 restraints weight = 26415.575| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26447 Z= 0.133 Angle : 0.708 15.226 36109 Z= 0.337 Chirality : 0.049 0.607 4220 Planarity : 0.005 0.064 4554 Dihedral : 7.583 103.310 4653 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 4.47 % Allowed : 25.91 % Favored : 69.62 % 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: -1.51 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 707 sheet: -1.01 (0.20), residues: 620 loop : -1.99 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 328 TYR 0.021 0.001 TYR A 369 PHE 0.019 0.001 PHE C 592 TRP 0.036 0.002 TRP C 633 HIS 0.007 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00302 (26349) covalent geometry : angle 0.64974 (35856) SS BOND : bond 0.00384 ( 38) SS BOND : angle 1.58252 ( 76) hydrogen bonds : bond 0.04040 ( 887) hydrogen bonds : angle 5.34894 ( 2466) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.00326 ( 15) link_BETA1-4 : angle 2.44835 ( 45) link_NAG-ASN : bond 0.00724 ( 44) link_NAG-ASN : angle 4.34598 ( 132) *********************** 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 260 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 136 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8753 (t80) cc_final: 0.8295 (m-80) REVERT: A 189 LEU cc_start: 0.9066 (tp) cc_final: 0.8862 (tt) REVERT: A 495 TYR cc_start: 0.3995 (OUTLIER) cc_final: 0.3700 (m-80) REVERT: A 630 THR cc_start: 0.8228 (m) cc_final: 0.7936 (m) REVERT: A 697 MET cc_start: 0.8654 (mmm) cc_final: 0.8302 (mmm) REVERT: A 896 ILE cc_start: 0.9049 (tp) cc_final: 0.8781 (tp) REVERT: B 54 LEU cc_start: 0.9006 (mm) cc_final: 0.8685 (mt) REVERT: B 102 ARG cc_start: 0.4200 (mtt180) cc_final: 0.3417 (mpt180) REVERT: B 164 ASN cc_start: 0.6091 (OUTLIER) cc_final: 0.5711 (p0) REVERT: B 200 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 204 TYR cc_start: 0.7019 (m-10) cc_final: 0.6451 (m-80) REVERT: B 495 TYR cc_start: 0.0781 (OUTLIER) cc_final: 0.0069 (t80) REVERT: B 697 MET cc_start: 0.8726 (mmm) cc_final: 0.8341 (tpp) REVERT: B 740 MET cc_start: 0.7837 (tpt) cc_final: 0.7599 (tpt) REVERT: B 869 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.7968 (pmm) REVERT: B 974 SER cc_start: 0.8972 (t) cc_final: 0.8446 (m) REVERT: C 300 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9149 (ttmt) REVERT: C 328 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6299 (ttp80) REVERT: C 378 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9278 (mmmt) REVERT: C 441 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6684 (tt) REVERT: C 532 ASN cc_start: 0.9044 (t0) cc_final: 0.8583 (p0) REVERT: C 726 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (mm) REVERT: C 756 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7603 (t80) REVERT: C 759 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: C 816 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7807 (m) REVERT: C 1005 GLN cc_start: 0.8541 (tp40) cc_final: 0.8306 (tp40) outliers start: 124 outliers final: 92 residues processed: 242 average time/residue: 0.1653 time to fit residues: 66.1772 Evaluate side-chains 230 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 126 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 307 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 251 optimal weight: 0.0870 chunk 261 optimal weight: 5.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.089681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062177 restraints weight = 96141.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064858 restraints weight = 58215.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065541 restraints weight = 34702.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066188 restraints weight = 28238.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066274 restraints weight = 25609.237| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26447 Z= 0.123 Angle : 0.692 14.930 36109 Z= 0.329 Chirality : 0.049 0.608 4220 Planarity : 0.004 0.058 4554 Dihedral : 7.378 101.993 4653 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 4.14 % Allowed : 26.34 % Favored : 69.51 % 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: -1.42 (0.15), residues: 3159 helix: 1.30 (0.20), residues: 710 sheet: -0.97 (0.20), residues: 618 loop : -1.94 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.027 0.001 TYR C 636 PHE 0.025 0.001 PHE B 92 TRP 0.034 0.001 TRP C 633 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00279 (26349) covalent geometry : angle 0.63504 (35856) SS BOND : bond 0.00434 ( 38) SS BOND : angle 1.51220 ( 76) hydrogen bonds : bond 0.03833 ( 887) hydrogen bonds : angle 5.16520 ( 2466) Misc. bond : bond 0.00029 ( 1) link_BETA1-4 : bond 0.00347 ( 15) link_BETA1-4 : angle 2.34147 ( 45) link_NAG-ASN : bond 0.00705 ( 44) link_NAG-ASN : angle 4.26721 ( 132) *********************** 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 255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 140 time to evaluate : 1.103 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 127 PHE cc_start: 0.8695 (t80) cc_final: 0.8286 (t80) REVERT: A 189 LEU cc_start: 0.9055 (tp) cc_final: 0.8842 (tt) REVERT: A 495 TYR cc_start: 0.4034 (OUTLIER) cc_final: 0.3706 (m-80) REVERT: A 630 THR cc_start: 0.8221 (m) cc_final: 0.7915 (m) REVERT: A 896 ILE cc_start: 0.9025 (tp) cc_final: 0.8776 (tp) REVERT: A 1029 MET cc_start: 0.7755 (tpp) cc_final: 0.7526 (tpp) REVERT: B 54 LEU cc_start: 0.8990 (mm) cc_final: 0.8699 (mt) REVERT: B 102 ARG cc_start: 0.4188 (mtt180) cc_final: 0.3466 (mpt180) REVERT: B 164 ASN cc_start: 0.6315 (OUTLIER) cc_final: 0.5861 (p0) REVERT: B 200 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7472 (t80) REVERT: B 204 TYR cc_start: 0.7227 (m-10) cc_final: 0.6650 (m-10) REVERT: B 495 TYR cc_start: 0.0678 (OUTLIER) cc_final: -0.0076 (t80) REVERT: B 697 MET cc_start: 0.8725 (mmm) cc_final: 0.8273 (tpt) REVERT: B 740 MET cc_start: 0.7889 (tpt) cc_final: 0.7666 (tpt) REVERT: B 869 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8001 (pmm) REVERT: C 328 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6145 (ttp80) REVERT: C 441 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6667 (tt) REVERT: C 532 ASN cc_start: 0.9043 (t0) cc_final: 0.8567 (p0) REVERT: C 726 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8553 (mm) REVERT: C 756 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7552 (t80) REVERT: C 759 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: C 816 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (m) REVERT: C 900 MET cc_start: 0.9051 (mmm) cc_final: 0.8221 (mmp) REVERT: C 973 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8119 (tp) REVERT: C 1005 GLN cc_start: 0.8490 (tp40) cc_final: 0.8244 (tp40) outliers start: 115 outliers final: 89 residues processed: 239 average time/residue: 0.1602 time to fit residues: 63.6498 Evaluate side-chains 232 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 131 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 242 optimal weight: 0.1980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.089126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062498 restraints weight = 96790.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064041 restraints weight = 58361.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064838 restraints weight = 37265.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065028 restraints weight = 35851.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065105 restraints weight = 30254.557| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26447 Z= 0.147 Angle : 0.698 15.304 36109 Z= 0.331 Chirality : 0.048 0.609 4220 Planarity : 0.005 0.059 4554 Dihedral : 7.279 102.602 4653 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 4.22 % Allowed : 26.27 % Favored : 69.51 % 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: -1.37 (0.15), residues: 3159 helix: 1.25 (0.20), residues: 715 sheet: -0.90 (0.20), residues: 619 loop : -1.89 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.025 0.001 TYR C 170 PHE 0.022 0.001 PHE B 92 TRP 0.033 0.001 TRP C 633 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00337 (26349) covalent geometry : angle 0.64339 (35856) SS BOND : bond 0.00401 ( 38) SS BOND : angle 1.54132 ( 76) hydrogen bonds : bond 0.03851 ( 887) hydrogen bonds : angle 5.15104 ( 2466) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00266 ( 15) link_BETA1-4 : angle 2.30399 ( 45) link_NAG-ASN : bond 0.00677 ( 44) link_NAG-ASN : angle 4.20925 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 139 time to evaluate : 1.072 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 127 PHE cc_start: 0.8775 (t80) cc_final: 0.8276 (t80) REVERT: A 177 MET cc_start: 0.6661 (mmp) cc_final: 0.4839 (ptt) REVERT: A 495 TYR cc_start: 0.3885 (OUTLIER) cc_final: 0.3632 (m-80) REVERT: A 630 THR cc_start: 0.8222 (m) cc_final: 0.7902 (m) REVERT: A 856 ASN cc_start: 0.8335 (p0) cc_final: 0.8133 (m110) REVERT: A 1031 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 54 LEU cc_start: 0.9047 (mm) cc_final: 0.8757 (mt) REVERT: B 102 ARG cc_start: 0.4247 (mtt180) cc_final: 0.3433 (mpt180) REVERT: B 164 ASN cc_start: 0.6151 (OUTLIER) cc_final: 0.5744 (p0) REVERT: B 189 LEU cc_start: 0.8758 (tt) cc_final: 0.8534 (mp) REVERT: B 200 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 204 TYR cc_start: 0.7240 (m-10) cc_final: 0.6720 (m-10) REVERT: B 495 TYR cc_start: 0.0442 (OUTLIER) cc_final: -0.0362 (t80) REVERT: B 697 MET cc_start: 0.8717 (mmm) cc_final: 0.8289 (tpt) REVERT: B 740 MET cc_start: 0.7892 (tpt) cc_final: 0.7657 (tpt) REVERT: B 855 PHE cc_start: 0.7230 (t80) cc_final: 0.6906 (t80) REVERT: B 869 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8005 (pmm) REVERT: B 974 SER cc_start: 0.9018 (t) cc_final: 0.8536 (m) REVERT: C 328 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6182 (ttp80) REVERT: C 532 ASN cc_start: 0.9060 (t0) cc_final: 0.8598 (p0) REVERT: C 726 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 756 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7550 (t80) REVERT: C 759 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: C 816 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7890 (m) REVERT: C 973 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8211 (tp) REVERT: C 1005 GLN cc_start: 0.8620 (tp40) cc_final: 0.8381 (tp40) outliers start: 117 outliers final: 92 residues processed: 241 average time/residue: 0.1583 time to fit residues: 63.6778 Evaluate side-chains 238 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 139 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 159 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 247 optimal weight: 0.4980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.089734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062692 restraints weight = 95254.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065055 restraints weight = 56962.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066045 restraints weight = 33856.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066504 restraints weight = 28179.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066650 restraints weight = 25771.282| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26447 Z= 0.120 Angle : 0.697 15.899 36109 Z= 0.328 Chirality : 0.048 0.610 4220 Planarity : 0.004 0.057 4554 Dihedral : 7.156 99.702 4653 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.56 % Rotamer: Outliers : 3.71 % Allowed : 26.70 % Favored : 69.59 % 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: -1.33 (0.15), residues: 3159 helix: 1.36 (0.20), residues: 707 sheet: -0.89 (0.21), residues: 619 loop : -1.88 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.026 0.001 TYR A 170 PHE 0.024 0.001 PHE B 92 TRP 0.035 0.001 TRP C 633 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00275 (26349) covalent geometry : angle 0.64468 (35856) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.41327 ( 76) hydrogen bonds : bond 0.03707 ( 887) hydrogen bonds : angle 5.06113 ( 2466) Misc. bond : bond 0.00024 ( 1) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 2.20385 ( 45) link_NAG-ASN : bond 0.00678 ( 44) link_NAG-ASN : angle 4.14387 ( 132) ********************** 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 243 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 140 time to evaluate : 0.990 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 127 PHE cc_start: 0.8648 (t80) cc_final: 0.8215 (t80) REVERT: A 177 MET cc_start: 0.6439 (mmp) cc_final: 0.4761 (ptt) REVERT: A 495 TYR cc_start: 0.3918 (OUTLIER) cc_final: 0.3640 (m-80) REVERT: A 630 THR cc_start: 0.8197 (m) cc_final: 0.7873 (m) REVERT: A 896 ILE cc_start: 0.8829 (tp) cc_final: 0.8601 (tp) REVERT: A 1029 MET cc_start: 0.7776 (tpp) cc_final: 0.7563 (tpp) REVERT: A 1031 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: B 52 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8418 (pm20) REVERT: B 54 LEU cc_start: 0.9063 (mm) cc_final: 0.8808 (mt) REVERT: B 102 ARG cc_start: 0.4309 (mtt180) cc_final: 0.3508 (mpt180) REVERT: B 164 ASN cc_start: 0.6142 (OUTLIER) cc_final: 0.5708 (p0) REVERT: B 200 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 204 TYR cc_start: 0.7205 (m-10) cc_final: 0.6573 (m-10) REVERT: B 495 TYR cc_start: 0.0434 (OUTLIER) cc_final: -0.0339 (t80) REVERT: B 697 MET cc_start: 0.8729 (mmm) cc_final: 0.8271 (tpt) REVERT: B 740 MET cc_start: 0.7946 (tpt) cc_final: 0.7611 (tpt) REVERT: B 869 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7935 (pmm) REVERT: B 974 SER cc_start: 0.8972 (t) cc_final: 0.8523 (m) REVERT: C 328 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6114 (ttp80) REVERT: C 532 ASN cc_start: 0.9064 (t0) cc_final: 0.8607 (p0) REVERT: C 726 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (mm) REVERT: C 756 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7479 (t80) REVERT: C 759 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: C 816 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7837 (m) REVERT: C 973 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8119 (tp) REVERT: C 1005 GLN cc_start: 0.8451 (tp40) cc_final: 0.8211 (tp40) outliers start: 103 outliers final: 83 residues processed: 229 average time/residue: 0.1596 time to fit residues: 60.9051 Evaluate side-chains 233 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 138 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 57 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 154 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.089130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062158 restraints weight = 94769.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064735 restraints weight = 57368.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065300 restraints weight = 34262.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065960 restraints weight = 28537.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066013 restraints weight = 25740.890| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26447 Z= 0.146 Angle : 0.706 16.689 36109 Z= 0.336 Chirality : 0.048 0.615 4220 Planarity : 0.004 0.052 4554 Dihedral : 7.136 101.063 4653 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 3.96 % Allowed : 26.45 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.15), residues: 3159 helix: 1.27 (0.20), residues: 717 sheet: -0.79 (0.20), residues: 622 loop : -1.85 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.025 0.001 TYR C 170 PHE 0.036 0.001 PHE A 592 TRP 0.035 0.001 TRP C 633 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00338 (26349) covalent geometry : angle 0.64788 (35856) SS BOND : bond 0.00410 ( 38) SS BOND : angle 2.46744 ( 76) hydrogen bonds : bond 0.03790 ( 887) hydrogen bonds : angle 5.09982 ( 2466) Misc. bond : bond 0.00024 ( 1) link_BETA1-4 : bond 0.00309 ( 15) link_BETA1-4 : angle 2.20178 ( 45) link_NAG-ASN : bond 0.00651 ( 44) link_NAG-ASN : angle 4.12262 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3950.04 seconds wall clock time: 69 minutes 42.60 seconds (4182.60 seconds total)