Starting phenix.real_space_refine on Sun Jun 22 19:25:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5q_38072/06_2025/8x5q_38072.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.066 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 111 5.16 5 C 16689 2.51 5 N 4278 2.21 5 O 5130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26208 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.58, per 1000 atoms: 0.59 Number of scatterers: 26208 At special positions: 0 Unit cell: (150, 140, 167, 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 111 16.00 O 5130 8.00 N 4278 7.00 C 16689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN C 122 " " NAG E 1 " - " ASN C 165 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN C 354 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 165 " " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN A 354 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 165 " " NAG T 1 " - " ASN B 234 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 354 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.2 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 51 sheets defined 21.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.712A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.660A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 884 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 941 removed outlier: 4.299A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.605A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.782A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.694A 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 826 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.646A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.586A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.460A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.584A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.722A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.579A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.535A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.466A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.593A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.339A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.603A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.571A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.259A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 317 removed outlier: 7.200A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.666A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.240A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.302A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.430A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.572A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.545A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'C' and resid 719 through 727 removed outlier: 7.606A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AB9, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.676A pdb=" N SER A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.070A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.250A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.221A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.621A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.166A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.384A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.334A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.574A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.566A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'A' and resid 719 through 727 removed outlier: 7.573A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'B' and resid 26 through 30 removed outlier: 3.660A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.083A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.114A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.526A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.143A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.052A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.336A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.437A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.332A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AF5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF6, first strand: chain 'B' and resid 1094 through 1097 826 hydrogen bonds defined for protein. 2238 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: 10.65 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8085 1.34 - 1.46: 6456 1.46 - 1.59: 12135 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" N VAL C 70 " pdb=" CA VAL C 70 " ideal model delta sigma weight residual 1.456 1.494 -0.037 9.50e-03 1.11e+04 1.53e+01 bond pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.52e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" N GLY B 566 " pdb=" CA GLY B 566 " ideal model delta sigma weight residual 1.444 1.479 -0.035 1.02e-02 9.61e+03 1.21e+01 bond pdb=" N PHE C 140 " pdb=" CA PHE C 140 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34294 1.64 - 3.28: 1962 3.28 - 4.92: 223 4.92 - 6.56: 35 6.56 - 8.20: 11 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR C 604 " pdb=" CA THR C 604 " pdb=" C THR C 604 " ideal model delta sigma weight residual 114.62 108.61 6.01 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 108.62 6.00 1.14e+00 7.69e-01 2.77e+01 angle pdb=" N GLN A 628 " pdb=" CA GLN A 628 " pdb=" C GLN A 628 " ideal model delta sigma weight residual 114.56 107.96 6.60 1.27e+00 6.20e-01 2.70e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 108.72 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" C PHE C 32 " pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " ideal model delta sigma weight residual 116.54 111.06 5.48 1.15e+00 7.56e-01 2.27e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 14934 22.60 - 45.20: 1395 45.20 - 67.80: 233 67.80 - 90.40: 89 90.40 - 113.00: 122 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 31.10 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 32.10 60.90 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3886 0.092 - 0.184: 413 0.184 - 0.276: 27 0.276 - 0.368: 4 0.368 - 0.460: 2 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.36e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.254 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" C7 NAG B1307 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.101 2.00e-02 2.50e+03 8.38e-02 8.77e+01 pdb=" C7 NAG A1306 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.134 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 190 " 0.741 9.50e-02 1.11e+02 3.32e-01 6.71e+01 pdb=" NE ARG A 190 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 190 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 190 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 190 " 0.022 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2155 2.74 - 3.28: 27214 3.28 - 3.82: 44072 3.82 - 4.36: 51547 4.36 - 4.90: 88873 Nonbonded interactions: 213861 Sorted by model distance: nonbonded pdb=" NH2 ARG B 34 " pdb=" O PRO B 217 " model vdw 2.198 3.120 nonbonded pdb=" O VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.201 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.207 3.040 ... (remaining 213856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 59.100 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.006 0.078 26913 Z= 0.355 Angle : 0.830 13.408 36786 Z= 0.493 Chirality : 0.054 0.460 4332 Planarity : 0.009 0.332 4650 Dihedral : 20.555 112.997 10569 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.41 % Rotamer: Outliers : 1.21 % Allowed : 22.41 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 624 sheet: -0.77 (0.20), residues: 636 loop : -2.14 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 633 HIS 0.004 0.001 HIS C 519 PHE 0.047 0.001 PHE C 643 TYR 0.035 0.002 TYR A 655 ARG 0.008 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 42) link_NAG-ASN : angle 2.19786 ( 126) link_BETA1-4 : bond 0.01009 ( 21) link_BETA1-4 : angle 4.16714 ( 63) hydrogen bonds : bond 0.20197 ( 816) hydrogen bonds : angle 7.80781 ( 2238) SS BOND : bond 0.00506 ( 36) SS BOND : angle 1.54772 ( 72) covalent geometry : bond 0.00560 (26814) covalent geometry : angle 0.80117 (36525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7038 (t0) cc_final: 0.6274 (p0) REVERT: C 141 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4314 (tt) REVERT: C 298 GLU cc_start: 0.8718 (tp30) cc_final: 0.8517 (tp30) REVERT: C 457 ARG cc_start: 0.6180 (mtp-110) cc_final: 0.5694 (mtp-110) REVERT: A 141 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6188 (mt) REVERT: A 655 TYR cc_start: 0.8361 (t80) cc_final: 0.8026 (t80) REVERT: B 582 LEU cc_start: 0.8435 (mp) cc_final: 0.8207 (pp) outliers start: 34 outliers final: 14 residues processed: 291 average time/residue: 0.4133 time to fit residues: 196.5752 Evaluate side-chains 227 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 580 GLN C 613 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN A 69 HIS A 321 GLN A 580 GLN A 613 GLN A 804 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 804 GLN B 955 ASN B1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098980 restraints weight = 50585.251| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.07 r_work: 0.3261 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26913 Z= 0.164 Angle : 0.751 21.242 36786 Z= 0.356 Chirality : 0.050 0.488 4332 Planarity : 0.004 0.069 4650 Dihedral : 15.277 97.746 4839 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.10 % Favored : 91.62 % Rotamer: Outliers : 3.51 % Allowed : 21.10 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3234 helix: 1.20 (0.21), residues: 609 sheet: -0.64 (0.19), residues: 648 loop : -2.02 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 633 HIS 0.004 0.001 HIS B 519 PHE 0.023 0.001 PHE C 168 TYR 0.023 0.002 TYR A1067 ARG 0.008 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 42) link_NAG-ASN : angle 3.34443 ( 126) link_BETA1-4 : bond 0.01309 ( 21) link_BETA1-4 : angle 4.12093 ( 63) hydrogen bonds : bond 0.04410 ( 816) hydrogen bonds : angle 5.97128 ( 2238) SS BOND : bond 0.00486 ( 36) SS BOND : angle 1.55706 ( 72) covalent geometry : bond 0.00370 (26814) covalent geometry : angle 0.70434 (36525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 235 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7429 (t0) cc_final: 0.6860 (m-40) REVERT: C 170 TYR cc_start: 0.7715 (t80) cc_final: 0.7265 (t80) REVERT: C 290 ASP cc_start: 0.8414 (t0) cc_final: 0.7986 (m-30) REVERT: C 298 GLU cc_start: 0.8681 (tp30) cc_final: 0.8469 (tp30) REVERT: C 377 PHE cc_start: 0.6685 (t80) cc_final: 0.6429 (t80) REVERT: C 655 TYR cc_start: 0.8412 (t80) cc_final: 0.7997 (t80) REVERT: C 754 LEU cc_start: 0.8624 (mt) cc_final: 0.8420 (tp) REVERT: C 988 GLU cc_start: 0.8250 (tt0) cc_final: 0.7868 (mt-10) REVERT: A 136 CYS cc_start: 0.6594 (t) cc_final: 0.6134 (p) REVERT: A 140 PHE cc_start: 0.6906 (p90) cc_final: 0.6515 (p90) REVERT: A 176 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.4111 (pt) REVERT: A 338 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7618 (t80) REVERT: A 377 PHE cc_start: 0.6532 (t80) cc_final: 0.6320 (t80) REVERT: A 655 TYR cc_start: 0.8326 (t80) cc_final: 0.8044 (t80) REVERT: A 1125 ASN cc_start: 0.7367 (t0) cc_final: 0.7067 (t0) REVERT: B 1031 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7904 (mt-10) outliers start: 99 outliers final: 50 residues processed: 315 average time/residue: 0.3139 time to fit residues: 166.5319 Evaluate side-chains 252 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 70 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 311 optimal weight: 0.7980 chunk 172 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 81 ASN C 245 HIS C1005 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 580 GLN B 895 GLN B1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100706 restraints weight = 50249.006| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.06 r_work: 0.3288 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26913 Z= 0.122 Angle : 0.680 18.418 36786 Z= 0.319 Chirality : 0.048 0.560 4332 Planarity : 0.004 0.064 4650 Dihedral : 12.562 93.560 4818 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 3.65 % Allowed : 21.95 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3234 helix: 1.38 (0.21), residues: 621 sheet: -0.55 (0.19), residues: 648 loop : -1.97 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.004 0.001 HIS B 245 PHE 0.014 0.001 PHE C 643 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 42) link_NAG-ASN : angle 3.23492 ( 126) link_BETA1-4 : bond 0.01307 ( 21) link_BETA1-4 : angle 4.01010 ( 63) hydrogen bonds : bond 0.03986 ( 816) hydrogen bonds : angle 5.63971 ( 2238) SS BOND : bond 0.00513 ( 36) SS BOND : angle 1.40890 ( 72) covalent geometry : bond 0.00265 (26814) covalent geometry : angle 0.63130 (36525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 238 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7798 (tt0) REVERT: C 118 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (tt) REVERT: C 137 ASN cc_start: 0.7253 (t0) cc_final: 0.6815 (m-40) REVERT: C 298 GLU cc_start: 0.8681 (tp30) cc_final: 0.8467 (tp30) REVERT: C 362 VAL cc_start: 0.8720 (p) cc_final: 0.8334 (m) REVERT: C 655 TYR cc_start: 0.8474 (t80) cc_final: 0.7992 (t80) REVERT: C 988 GLU cc_start: 0.8359 (tt0) cc_final: 0.8058 (mt-10) REVERT: C 1050 MET cc_start: 0.8679 (ptt) cc_final: 0.8397 (ptp) REVERT: A 136 CYS cc_start: 0.6337 (t) cc_final: 0.6045 (p) REVERT: A 176 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3886 (pt) REVERT: A 338 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7533 (t80) REVERT: A 655 TYR cc_start: 0.8408 (t80) cc_final: 0.8100 (t80) REVERT: A 1125 ASN cc_start: 0.7156 (t0) cc_final: 0.6775 (t0) REVERT: B 197 ILE cc_start: 0.7555 (tp) cc_final: 0.7326 (tt) REVERT: B 309 GLU cc_start: 0.8116 (pm20) cc_final: 0.7907 (mp0) REVERT: B 633 TRP cc_start: 0.7642 (p-90) cc_final: 0.7300 (p-90) REVERT: B 1031 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7928 (mt-10) outliers start: 103 outliers final: 55 residues processed: 314 average time/residue: 0.3284 time to fit residues: 176.7245 Evaluate side-chains 254 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.0770 chunk 132 optimal weight: 5.9990 chunk 22 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 239 GLN B 493 GLN B 613 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093155 restraints weight = 50962.615| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.10 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26913 Z= 0.207 Angle : 0.729 18.962 36786 Z= 0.346 Chirality : 0.050 0.449 4332 Planarity : 0.004 0.071 4650 Dihedral : 10.896 88.434 4818 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.60 % Favored : 91.37 % Rotamer: Outliers : 4.93 % Allowed : 21.24 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3234 helix: 1.09 (0.21), residues: 618 sheet: -0.54 (0.19), residues: 618 loop : -1.93 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 633 HIS 0.005 0.001 HIS B 519 PHE 0.021 0.002 PHE C 823 TYR 0.025 0.002 TYR C 380 ARG 0.007 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 42) link_NAG-ASN : angle 3.30313 ( 126) link_BETA1-4 : bond 0.01155 ( 21) link_BETA1-4 : angle 3.95673 ( 63) hydrogen bonds : bond 0.04230 ( 816) hydrogen bonds : angle 5.58213 ( 2238) SS BOND : bond 0.00476 ( 36) SS BOND : angle 1.93454 ( 72) covalent geometry : bond 0.00495 (26814) covalent geometry : angle 0.68047 (36525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 202 time to evaluate : 2.937 Fit side-chains revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (tt) REVERT: C 137 ASN cc_start: 0.7518 (t0) cc_final: 0.6706 (m-40) REVERT: C 170 TYR cc_start: 0.8042 (t80) cc_final: 0.7652 (t80) REVERT: C 229 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.6019 (pp) REVERT: C 265 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.4771 (t80) REVERT: C 266 TYR cc_start: 0.8351 (m-80) cc_final: 0.8099 (m-80) REVERT: C 298 GLU cc_start: 0.8730 (tp30) cc_final: 0.8427 (tp30) REVERT: C 655 TYR cc_start: 0.8639 (t80) cc_final: 0.7955 (t80) REVERT: C 981 LEU cc_start: 0.8596 (mt) cc_final: 0.8394 (mt) REVERT: C 988 GLU cc_start: 0.8409 (tt0) cc_final: 0.8033 (mt-10) REVERT: C 1050 MET cc_start: 0.8861 (ptt) cc_final: 0.8534 (ptp) REVERT: C 1125 ASN cc_start: 0.7213 (t0) cc_final: 0.6516 (t0) REVERT: A 136 CYS cc_start: 0.6651 (t) cc_final: 0.6249 (p) REVERT: A 176 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4078 (pt) REVERT: A 265 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5758 (t80) REVERT: A 655 TYR cc_start: 0.8612 (t80) cc_final: 0.8140 (t80) REVERT: A 754 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 764 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7066 (ttpp) REVERT: A 994 ASP cc_start: 0.8605 (t0) cc_final: 0.8381 (t0) REVERT: A 1125 ASN cc_start: 0.7409 (t0) cc_final: 0.6894 (t0) REVERT: B 265 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.4820 (t80) REVERT: B 290 ASP cc_start: 0.8461 (t0) cc_final: 0.8237 (m-30) REVERT: B 633 TRP cc_start: 0.7900 (p-90) cc_final: 0.7533 (p-90) REVERT: B 1031 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 1125 ASN cc_start: 0.7349 (t0) cc_final: 0.6741 (t0) outliers start: 139 outliers final: 82 residues processed: 317 average time/residue: 0.3278 time to fit residues: 176.3590 Evaluate side-chains 260 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 169 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 133 optimal weight: 4.9990 chunk 240 optimal weight: 0.2980 chunk 170 optimal weight: 0.7980 chunk 271 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 281 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 409 GLN A 751 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094444 restraints weight = 50259.282| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.06 r_work: 0.3180 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 26913 Z= 0.146 Angle : 0.675 19.031 36786 Z= 0.321 Chirality : 0.048 0.478 4332 Planarity : 0.004 0.072 4650 Dihedral : 10.182 85.936 4818 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.26 % Allowed : 21.63 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3234 helix: 1.10 (0.21), residues: 636 sheet: -0.43 (0.19), residues: 603 loop : -1.98 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.004 0.001 HIS B1088 PHE 0.014 0.001 PHE A 823 TYR 0.018 0.001 TYR C 380 ARG 0.004 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 42) link_NAG-ASN : angle 3.15311 ( 126) link_BETA1-4 : bond 0.01218 ( 21) link_BETA1-4 : angle 3.87083 ( 63) hydrogen bonds : bond 0.03794 ( 816) hydrogen bonds : angle 5.48468 ( 2238) SS BOND : bond 0.00472 ( 36) SS BOND : angle 2.14844 ( 72) covalent geometry : bond 0.00337 (26814) covalent geometry : angle 0.62468 (36525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 195 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8313 (tt) REVERT: C 137 ASN cc_start: 0.7492 (t0) cc_final: 0.6680 (m-40) REVERT: C 170 TYR cc_start: 0.8084 (t80) cc_final: 0.7604 (t80) REVERT: C 229 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5928 (pp) REVERT: C 265 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4604 (t80) REVERT: C 266 TYR cc_start: 0.8280 (m-80) cc_final: 0.8069 (m-80) REVERT: C 298 GLU cc_start: 0.8687 (tp30) cc_final: 0.8396 (tp30) REVERT: C 655 TYR cc_start: 0.8617 (t80) cc_final: 0.8072 (t80) REVERT: C 754 LEU cc_start: 0.8764 (tp) cc_final: 0.8354 (mp) REVERT: C 1050 MET cc_start: 0.8856 (ptt) cc_final: 0.8595 (ptp) REVERT: C 1125 ASN cc_start: 0.7327 (t0) cc_final: 0.6612 (t0) REVERT: A 40 ASP cc_start: 0.7739 (m-30) cc_final: 0.6963 (p0) REVERT: A 136 CYS cc_start: 0.6692 (t) cc_final: 0.6271 (p) REVERT: A 265 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.5224 (t80) REVERT: A 298 GLU cc_start: 0.8659 (tp30) cc_final: 0.8437 (tp30) REVERT: A 633 TRP cc_start: 0.7752 (p-90) cc_final: 0.7520 (p-90) REVERT: A 655 TYR cc_start: 0.8640 (t80) cc_final: 0.8183 (t80) REVERT: A 754 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 917 TYR cc_start: 0.8647 (m-80) cc_final: 0.8418 (m-80) REVERT: A 994 ASP cc_start: 0.8679 (t0) cc_final: 0.8392 (t0) REVERT: A 1125 ASN cc_start: 0.7170 (t0) cc_final: 0.6596 (t0) REVERT: B 265 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.4446 (t80) REVERT: B 633 TRP cc_start: 0.7939 (p-90) cc_final: 0.7600 (p-90) REVERT: B 1031 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 1125 ASN cc_start: 0.7276 (t0) cc_final: 0.6639 (t0) outliers start: 120 outliers final: 76 residues processed: 287 average time/residue: 0.3262 time to fit residues: 160.9806 Evaluate side-chains 254 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 171 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 247 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 271 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 244 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.123506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093399 restraints weight = 50137.568| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.06 r_work: 0.3163 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26913 Z= 0.154 Angle : 0.672 19.014 36786 Z= 0.319 Chirality : 0.048 0.449 4332 Planarity : 0.004 0.076 4650 Dihedral : 9.346 82.602 4816 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.57 % Allowed : 21.67 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3234 helix: 1.11 (0.21), residues: 636 sheet: -0.43 (0.20), residues: 573 loop : -1.98 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 633 HIS 0.003 0.001 HIS A1088 PHE 0.012 0.001 PHE A 823 TYR 0.020 0.001 TYR C 380 ARG 0.004 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 42) link_NAG-ASN : angle 3.18090 ( 126) link_BETA1-4 : bond 0.01190 ( 21) link_BETA1-4 : angle 3.78624 ( 63) hydrogen bonds : bond 0.03747 ( 816) hydrogen bonds : angle 5.38866 ( 2238) SS BOND : bond 0.00463 ( 36) SS BOND : angle 1.86688 ( 72) covalent geometry : bond 0.00362 (26814) covalent geometry : angle 0.62291 (36525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 177 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 170 TYR cc_start: 0.8046 (t80) cc_final: 0.7552 (t80) REVERT: C 229 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6207 (pp) REVERT: C 265 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.4777 (t80) REVERT: C 298 GLU cc_start: 0.8679 (tp30) cc_final: 0.8376 (tp30) REVERT: C 462 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8599 (mtmm) REVERT: C 582 LEU cc_start: 0.8660 (mp) cc_final: 0.8384 (pp) REVERT: C 655 TYR cc_start: 0.8658 (t80) cc_final: 0.8095 (t80) REVERT: C 754 LEU cc_start: 0.8786 (tp) cc_final: 0.8366 (mp) REVERT: C 1050 MET cc_start: 0.8909 (ptt) cc_final: 0.8662 (ptp) REVERT: C 1125 ASN cc_start: 0.7476 (t0) cc_final: 0.6667 (t0) REVERT: A 40 ASP cc_start: 0.7815 (m-30) cc_final: 0.7231 (p0) REVERT: A 136 CYS cc_start: 0.6728 (t) cc_final: 0.6418 (p) REVERT: A 176 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.4018 (pt) REVERT: A 265 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5496 (t80) REVERT: A 298 GLU cc_start: 0.8684 (tp30) cc_final: 0.8453 (tp30) REVERT: A 462 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8488 (mtmm) REVERT: A 633 TRP cc_start: 0.7847 (p-90) cc_final: 0.7633 (p-90) REVERT: A 655 TYR cc_start: 0.8602 (t80) cc_final: 0.8213 (t80) REVERT: A 754 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 764 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7122 (ttpp) REVERT: A 994 ASP cc_start: 0.8697 (t0) cc_final: 0.8488 (t0) REVERT: A 1125 ASN cc_start: 0.7357 (t0) cc_final: 0.6718 (t0) REVERT: B 201 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.5088 (m-80) REVERT: B 265 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4618 (t80) REVERT: B 388 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8032 (m110) REVERT: B 633 TRP cc_start: 0.8070 (p-90) cc_final: 0.7704 (p-90) REVERT: B 1031 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: B 1125 ASN cc_start: 0.7364 (t0) cc_final: 0.6724 (t0) outliers start: 129 outliers final: 90 residues processed: 284 average time/residue: 0.3073 time to fit residues: 150.8616 Evaluate side-chains 254 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 153 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 285 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 0.0270 chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B1036 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 = 0.3777 r_free = 0.3777 target = 0.124201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094294 restraints weight = 50159.214| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.07 r_work: 0.3178 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26913 Z= 0.127 Angle : 0.651 18.952 36786 Z= 0.309 Chirality : 0.047 0.434 4332 Planarity : 0.004 0.079 4650 Dihedral : 8.693 80.214 4816 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.01 % Allowed : 22.62 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3234 helix: 1.22 (0.21), residues: 636 sheet: -0.50 (0.20), residues: 588 loop : -1.94 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 633 HIS 0.004 0.001 HIS C1088 PHE 0.013 0.001 PHE B 643 TYR 0.017 0.001 TYR C 380 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 42) link_NAG-ASN : angle 3.13369 ( 126) link_BETA1-4 : bond 0.01220 ( 21) link_BETA1-4 : angle 3.73212 ( 63) hydrogen bonds : bond 0.03649 ( 816) hydrogen bonds : angle 5.35570 ( 2238) SS BOND : bond 0.00475 ( 36) SS BOND : angle 1.53363 ( 72) covalent geometry : bond 0.00292 (26814) covalent geometry : angle 0.60392 (36525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 174 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8292 (tt) REVERT: C 170 TYR cc_start: 0.8111 (t80) cc_final: 0.7636 (t80) REVERT: C 229 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6205 (pp) REVERT: C 266 TYR cc_start: 0.8178 (m-80) cc_final: 0.7964 (m-80) REVERT: C 298 GLU cc_start: 0.8654 (tp30) cc_final: 0.8356 (tp30) REVERT: C 394 ASN cc_start: 0.7533 (t0) cc_final: 0.7234 (t0) REVERT: C 582 LEU cc_start: 0.8620 (mp) cc_final: 0.8345 (pp) REVERT: C 655 TYR cc_start: 0.8637 (t80) cc_final: 0.8115 (t80) REVERT: C 1050 MET cc_start: 0.8898 (ptt) cc_final: 0.8650 (ptp) REVERT: C 1125 ASN cc_start: 0.7462 (t0) cc_final: 0.6610 (t0) REVERT: A 40 ASP cc_start: 0.7833 (m-30) cc_final: 0.7463 (p0) REVERT: A 136 CYS cc_start: 0.6775 (t) cc_final: 0.6330 (p) REVERT: A 176 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4033 (pt) REVERT: A 265 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.5303 (t80) REVERT: A 298 GLU cc_start: 0.8663 (tp30) cc_final: 0.8434 (tp30) REVERT: A 462 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8474 (mtmm) REVERT: A 633 TRP cc_start: 0.7937 (p-90) cc_final: 0.7701 (p-90) REVERT: A 655 TYR cc_start: 0.8596 (t80) cc_final: 0.8302 (t80) REVERT: A 754 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 994 ASP cc_start: 0.8615 (t0) cc_final: 0.8374 (t0) REVERT: A 1028 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9036 (mttm) REVERT: A 1125 ASN cc_start: 0.7274 (t0) cc_final: 0.6619 (t0) REVERT: B 201 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.5193 (m-80) REVERT: B 388 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8017 (m110) REVERT: B 633 TRP cc_start: 0.8010 (p-90) cc_final: 0.7689 (p-90) REVERT: B 1031 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: B 1125 ASN cc_start: 0.7371 (t0) cc_final: 0.6696 (t0) outliers start: 113 outliers final: 86 residues processed: 268 average time/residue: 0.3137 time to fit residues: 144.5117 Evaluate side-chains 253 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 158 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 161 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 0.2980 chunk 146 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B1036 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 = 0.3762 r_free = 0.3762 target = 0.123173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093060 restraints weight = 50252.974| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.09 r_work: 0.3154 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26913 Z= 0.145 Angle : 0.653 18.945 36786 Z= 0.311 Chirality : 0.047 0.416 4332 Planarity : 0.004 0.077 4650 Dihedral : 7.999 77.303 4816 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.26 % Allowed : 22.62 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3234 helix: 1.18 (0.21), residues: 636 sheet: -0.51 (0.20), residues: 588 loop : -1.92 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 633 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE B 643 TYR 0.019 0.001 TYR C 380 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 42) link_NAG-ASN : angle 3.17025 ( 126) link_BETA1-4 : bond 0.01187 ( 21) link_BETA1-4 : angle 3.67162 ( 63) hydrogen bonds : bond 0.03722 ( 816) hydrogen bonds : angle 5.33514 ( 2238) SS BOND : bond 0.00403 ( 36) SS BOND : angle 1.57757 ( 72) covalent geometry : bond 0.00340 (26814) covalent geometry : angle 0.60531 (36525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 174 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8344 (tt) REVERT: C 170 TYR cc_start: 0.8102 (t80) cc_final: 0.7594 (t80) REVERT: C 229 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6466 (pp) REVERT: C 265 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.4827 (t80) REVERT: C 266 TYR cc_start: 0.8345 (m-80) cc_final: 0.8098 (m-80) REVERT: C 298 GLU cc_start: 0.8652 (tp30) cc_final: 0.8352 (tp30) REVERT: C 582 LEU cc_start: 0.8658 (mp) cc_final: 0.8398 (pp) REVERT: C 655 TYR cc_start: 0.8670 (t80) cc_final: 0.8113 (t80) REVERT: C 1050 MET cc_start: 0.8923 (ptt) cc_final: 0.8704 (ptp) REVERT: C 1125 ASN cc_start: 0.7514 (t0) cc_final: 0.6614 (t0) REVERT: A 176 LEU cc_start: 0.4560 (OUTLIER) cc_final: 0.4109 (pt) REVERT: A 265 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5503 (t80) REVERT: A 298 GLU cc_start: 0.8711 (tp30) cc_final: 0.8465 (tp30) REVERT: A 365 TYR cc_start: 0.8657 (m-80) cc_final: 0.8454 (m-80) REVERT: A 655 TYR cc_start: 0.8611 (t80) cc_final: 0.8408 (t80) REVERT: A 754 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 994 ASP cc_start: 0.8740 (t0) cc_final: 0.8475 (t0) REVERT: A 1028 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9036 (mttm) REVERT: A 1125 ASN cc_start: 0.7213 (t0) cc_final: 0.6444 (t0) REVERT: B 52 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 201 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: B 265 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.4881 (t80) REVERT: B 633 TRP cc_start: 0.8098 (p-90) cc_final: 0.7799 (p-90) REVERT: B 752 LEU cc_start: 0.9171 (tt) cc_final: 0.8861 (tt) REVERT: B 1031 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: B 1125 ASN cc_start: 0.7414 (t0) cc_final: 0.6661 (t0) outliers start: 120 outliers final: 93 residues processed: 273 average time/residue: 0.3095 time to fit residues: 145.7303 Evaluate side-chains 268 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 165 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 317 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 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 = 0.3768 r_free = 0.3768 target = 0.123509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093438 restraints weight = 50510.515| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.10 r_work: 0.3162 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26913 Z= 0.131 Angle : 0.647 18.968 36786 Z= 0.307 Chirality : 0.046 0.413 4332 Planarity : 0.004 0.078 4650 Dihedral : 7.601 75.489 4816 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.01 % Allowed : 23.09 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3234 helix: 1.25 (0.21), residues: 630 sheet: -0.48 (0.21), residues: 588 loop : -1.90 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.003 0.001 HIS A1088 PHE 0.015 0.001 PHE B 643 TYR 0.017 0.001 TYR C 380 ARG 0.004 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 42) link_NAG-ASN : angle 3.14504 ( 126) link_BETA1-4 : bond 0.01200 ( 21) link_BETA1-4 : angle 3.65808 ( 63) hydrogen bonds : bond 0.03651 ( 816) hydrogen bonds : angle 5.31510 ( 2238) SS BOND : bond 0.00438 ( 36) SS BOND : angle 1.56376 ( 72) covalent geometry : bond 0.00301 (26814) covalent geometry : angle 0.59919 (36525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 173 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 170 TYR cc_start: 0.8118 (t80) cc_final: 0.7623 (t80) REVERT: C 229 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6489 (pp) REVERT: C 265 TYR cc_start: 0.5866 (OUTLIER) cc_final: 0.4759 (t80) REVERT: C 266 TYR cc_start: 0.8288 (m-80) cc_final: 0.8077 (m-80) REVERT: C 298 GLU cc_start: 0.8643 (tp30) cc_final: 0.8352 (tp30) REVERT: C 394 ASN cc_start: 0.7480 (t0) cc_final: 0.7230 (t0) REVERT: C 582 LEU cc_start: 0.8648 (mp) cc_final: 0.8318 (pp) REVERT: C 655 TYR cc_start: 0.8667 (t80) cc_final: 0.8133 (t80) REVERT: C 1050 MET cc_start: 0.8943 (ptt) cc_final: 0.8726 (ptp) REVERT: C 1125 ASN cc_start: 0.7579 (t0) cc_final: 0.6680 (t0) REVERT: A 176 LEU cc_start: 0.4531 (OUTLIER) cc_final: 0.4079 (pt) REVERT: A 265 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.5359 (t80) REVERT: A 365 TYR cc_start: 0.8571 (m-80) cc_final: 0.8314 (m-80) REVERT: A 754 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 878 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 994 ASP cc_start: 0.8703 (t0) cc_final: 0.8473 (t0) REVERT: A 1028 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8999 (mttm) REVERT: A 1125 ASN cc_start: 0.7366 (t0) cc_final: 0.6595 (t0) REVERT: B 201 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5939 (m-80) REVERT: B 265 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5003 (t80) REVERT: B 633 TRP cc_start: 0.8036 (p-90) cc_final: 0.7763 (p-90) REVERT: B 752 LEU cc_start: 0.9163 (tt) cc_final: 0.8810 (tt) REVERT: B 878 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8446 (tt) REVERT: B 1031 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 1125 ASN cc_start: 0.7480 (t0) cc_final: 0.6737 (t0) outliers start: 113 outliers final: 92 residues processed: 263 average time/residue: 0.4256 time to fit residues: 195.3562 Evaluate side-chains 263 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 159 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 40 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 290 optimal weight: 0.4980 chunk 271 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 146 optimal weight: 0.0070 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A1036 GLN B 493 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090494 restraints weight = 50059.613| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.04 r_work: 0.3113 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26913 Z= 0.188 Angle : 0.686 18.990 36786 Z= 0.330 Chirality : 0.048 0.398 4332 Planarity : 0.004 0.078 4650 Dihedral : 7.179 73.481 4816 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.15 % Allowed : 23.26 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3234 helix: 1.04 (0.21), residues: 636 sheet: -0.58 (0.21), residues: 570 loop : -1.91 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.019 0.001 PHE B 643 TYR 0.023 0.002 TYR C 380 ARG 0.004 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 42) link_NAG-ASN : angle 3.24095 ( 126) link_BETA1-4 : bond 0.01155 ( 21) link_BETA1-4 : angle 3.66079 ( 63) hydrogen bonds : bond 0.03883 ( 816) hydrogen bonds : angle 5.37623 ( 2238) SS BOND : bond 0.00585 ( 36) SS BOND : angle 1.82225 ( 72) covalent geometry : bond 0.00449 (26814) covalent geometry : angle 0.63912 (36525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 154 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8478 (tt) REVERT: C 170 TYR cc_start: 0.8180 (t80) cc_final: 0.7678 (t80) REVERT: C 265 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5099 (t80) REVERT: C 266 TYR cc_start: 0.8392 (m-80) cc_final: 0.8066 (m-80) REVERT: C 298 GLU cc_start: 0.8652 (tp30) cc_final: 0.8353 (tp30) REVERT: C 582 LEU cc_start: 0.8722 (mp) cc_final: 0.8489 (pp) REVERT: C 655 TYR cc_start: 0.8674 (t80) cc_final: 0.8130 (t80) REVERT: C 1050 MET cc_start: 0.8972 (ptt) cc_final: 0.8751 (ptp) REVERT: C 1125 ASN cc_start: 0.7724 (t0) cc_final: 0.6932 (t0) REVERT: A 176 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4335 (pt) REVERT: A 265 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5704 (t80) REVERT: A 365 TYR cc_start: 0.8669 (m-80) cc_final: 0.8376 (m-80) REVERT: A 754 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 878 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 994 ASP cc_start: 0.8660 (t0) cc_final: 0.8419 (t0) REVERT: A 1125 ASN cc_start: 0.7709 (t0) cc_final: 0.6932 (t0) REVERT: B 201 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: B 265 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5296 (t80) REVERT: B 633 TRP cc_start: 0.8042 (p-90) cc_final: 0.7704 (p-90) REVERT: B 752 LEU cc_start: 0.9173 (tt) cc_final: 0.8912 (tt) REVERT: B 1031 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: B 1125 ASN cc_start: 0.7603 (t0) cc_final: 0.6847 (t0) outliers start: 117 outliers final: 91 residues processed: 252 average time/residue: 0.5709 time to fit residues: 251.7665 Evaluate side-chains 247 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 147 time to evaluate : 7.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 58 optimal weight: 20.0000 chunk 306 optimal weight: 0.0030 chunk 193 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 264 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 163 optimal weight: 0.0370 chunk 299 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 563 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 317 ASN B 493 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.123613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.093917 restraints weight = 49848.349| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.05 r_work: 0.3167 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26913 Z= 0.116 Angle : 0.644 19.010 36786 Z= 0.310 Chirality : 0.046 0.407 4332 Planarity : 0.004 0.079 4650 Dihedral : 6.874 71.469 4816 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.33 % Allowed : 24.04 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3234 helix: 1.18 (0.21), residues: 630 sheet: -0.46 (0.21), residues: 588 loop : -1.88 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.015 0.001 PHE B 643 TYR 0.015 0.001 TYR B 265 ARG 0.006 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 42) link_NAG-ASN : angle 3.13118 ( 126) link_BETA1-4 : bond 0.01194 ( 21) link_BETA1-4 : angle 3.62604 ( 63) hydrogen bonds : bond 0.03585 ( 816) hydrogen bonds : angle 5.35262 ( 2238) SS BOND : bond 0.00511 ( 36) SS BOND : angle 1.52945 ( 72) covalent geometry : bond 0.00262 (26814) covalent geometry : angle 0.59738 (36525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11421.64 seconds wall clock time: 204 minutes 2.94 seconds (12242.94 seconds total)