Starting phenix.real_space_refine on Sun May 25 03:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5q_38072/05_2025/8x5q_38072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5q_38072/05_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_38072/05_2025/8x5q_38072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5q_38072/05_2025/8x5q_38072.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5q_38072/05_2025/8x5q_38072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5q_38072/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.69, per 1000 atoms: 0.56 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: 6.88 Conformation dependent library (CDL) restraints added in 3.4 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: 4.02 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: 13.66 Time building geometry restraints manager: 7.96 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.120 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 62.110 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.380 ------------------------------------------------------------------------------- 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 : 2.772 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: 0.3456 time to fit residues: 164.1641 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 : 2.727 ------------------------------------------------------------------------------- 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 = 50585.245| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.07 r_work: 0.3260 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 137 ASN cc_start: 0.7432 (t0) cc_final: 0.6860 (m-40) REVERT: C 170 TYR cc_start: 0.7716 (t80) cc_final: 0.7268 (t80) REVERT: C 290 ASP cc_start: 0.8417 (t0) cc_final: 0.7988 (m-30) REVERT: C 298 GLU cc_start: 0.8680 (tp30) cc_final: 0.8469 (tp30) REVERT: C 377 PHE cc_start: 0.6683 (t80) cc_final: 0.6426 (t80) REVERT: C 655 TYR cc_start: 0.8412 (t80) cc_final: 0.8000 (t80) REVERT: C 754 LEU cc_start: 0.8628 (mt) cc_final: 0.8425 (tp) REVERT: C 988 GLU cc_start: 0.8250 (tt0) cc_final: 0.7871 (mt-10) REVERT: A 136 CYS cc_start: 0.6600 (t) cc_final: 0.6136 (p) REVERT: A 140 PHE cc_start: 0.6908 (p90) cc_final: 0.6516 (p90) REVERT: A 176 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4110 (pt) REVERT: A 338 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 377 PHE cc_start: 0.6532 (t80) cc_final: 0.6316 (t80) REVERT: A 655 TYR cc_start: 0.8323 (t80) cc_final: 0.8043 (t80) REVERT: A 1125 ASN cc_start: 0.7368 (t0) cc_final: 0.7068 (t0) REVERT: B 1031 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7906 (mt-10) outliers start: 99 outliers final: 50 residues processed: 315 average time/residue: 0.3209 time to fit residues: 170.8740 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 : 2.655 ------------------------------------------------------------------------------- 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: 0.9990 chunk 262 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 311 optimal weight: 0.7980 chunk 172 optimal weight: 0.0050 chunk 39 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.5574 ------------------------------------------------------------------------------- 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 ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.129132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099565 restraints weight = 50222.071| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.06 r_work: 0.3271 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26913 Z= 0.127 Angle : 0.685 18.446 36786 Z= 0.322 Chirality : 0.049 0.549 4332 Planarity : 0.004 0.067 4650 Dihedral : 12.767 94.144 4818 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.70 % Favored : 92.15 % Rotamer: Outliers : 3.62 % Allowed : 22.16 % Favored : 74.22 % 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: -1.43 (0.14), residues: 3234 helix: 1.36 (0.21), residues: 618 sheet: -0.58 (0.19), residues: 648 loop : -1.95 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.004 0.001 HIS B1088 PHE 0.014 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 42) link_NAG-ASN : angle 3.25235 ( 126) link_BETA1-4 : bond 0.01225 ( 21) link_BETA1-4 : angle 4.02473 ( 63) hydrogen bonds : bond 0.03982 ( 816) hydrogen bonds : angle 5.67190 ( 2238) SS BOND : bond 0.00587 ( 36) SS BOND : angle 1.43504 ( 72) covalent geometry : bond 0.00282 (26814) covalent geometry : angle 0.63604 (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 329 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 227 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (tt) REVERT: C 137 ASN cc_start: 0.7362 (t0) cc_final: 0.6884 (m-40) REVERT: C 290 ASP cc_start: 0.8354 (t0) cc_final: 0.7993 (m-30) REVERT: C 298 GLU cc_start: 0.8681 (tp30) cc_final: 0.8467 (tp30) REVERT: C 655 TYR cc_start: 0.8465 (t80) cc_final: 0.8006 (t80) REVERT: C 988 GLU cc_start: 0.8334 (tt0) cc_final: 0.8027 (mt-10) REVERT: C 1050 MET cc_start: 0.8672 (ptt) cc_final: 0.8397 (ptp) REVERT: A 136 CYS cc_start: 0.6400 (t) cc_final: 0.6072 (p) REVERT: A 176 LEU cc_start: 0.4328 (OUTLIER) cc_final: 0.3915 (pt) REVERT: A 338 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 655 TYR cc_start: 0.8426 (t80) cc_final: 0.8114 (t80) REVERT: A 1125 ASN cc_start: 0.7299 (t0) cc_final: 0.6928 (t0) REVERT: B 197 ILE cc_start: 0.7559 (tp) cc_final: 0.7325 (tt) REVERT: B 309 GLU cc_start: 0.8126 (pm20) cc_final: 0.7909 (mp0) REVERT: B 1031 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 102 outliers final: 59 residues processed: 304 average time/residue: 0.3109 time to fit residues: 161.9408 Evaluate side-chains 257 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 780 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE 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 902 MET 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 512 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 1055 SER 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: 10.0000 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.0270 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: 5.9990 chunk 166 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 239 GLN B 321 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087713 restraints weight = 51207.777| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.10 r_work: 0.3058 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 26913 Z= 0.321 Angle : 0.845 18.522 36786 Z= 0.407 Chirality : 0.053 0.417 4332 Planarity : 0.005 0.075 4650 Dihedral : 11.385 90.839 4818 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.62 % Favored : 90.35 % Rotamer: Outliers : 6.21 % Allowed : 20.18 % Favored : 73.62 % 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: -1.85 (0.14), residues: 3234 helix: 0.58 (0.21), residues: 618 sheet: -0.61 (0.19), residues: 594 loop : -2.14 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 633 HIS 0.007 0.002 HIS B1064 PHE 0.027 0.002 PHE B 168 TYR 0.034 0.003 TYR C 380 ARG 0.008 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 42) link_NAG-ASN : angle 3.53132 ( 126) link_BETA1-4 : bond 0.01107 ( 21) link_BETA1-4 : angle 4.00523 ( 63) hydrogen bonds : bond 0.04921 ( 816) hydrogen bonds : angle 5.91104 ( 2238) SS BOND : bond 0.00643 ( 36) SS BOND : angle 2.42713 ( 72) covalent geometry : bond 0.00776 (26814) covalent geometry : angle 0.79784 (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 357 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 182 time to evaluate : 2.780 Fit side-chains REVERT: C 118 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 229 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6790 (pp) REVERT: C 265 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.5546 (t80) REVERT: C 266 TYR cc_start: 0.8528 (m-80) cc_final: 0.7987 (m-80) REVERT: C 655 TYR cc_start: 0.8713 (t80) cc_final: 0.7985 (t80) REVERT: C 895 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: C 988 GLU cc_start: 0.8490 (tt0) cc_final: 0.8026 (mt-10) REVERT: C 1050 MET cc_start: 0.8992 (ptt) cc_final: 0.8644 (ptp) REVERT: C 1125 ASN cc_start: 0.7630 (t0) cc_final: 0.6861 (t0) REVERT: A 176 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4233 (pt) REVERT: A 265 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.5970 (t80) REVERT: A 338 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8159 (t80) REVERT: A 346 ARG cc_start: 0.6766 (mmm160) cc_final: 0.6393 (ttm-80) REVERT: A 633 TRP cc_start: 0.8049 (p-90) cc_final: 0.7765 (p-90) REVERT: A 655 TYR cc_start: 0.8680 (t80) cc_final: 0.8052 (t80) REVERT: A 754 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 764 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: A 878 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 1125 ASN cc_start: 0.7678 (t0) cc_final: 0.7052 (t0) REVERT: B 229 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6549 (pp) REVERT: B 265 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 266 TYR cc_start: 0.8607 (m-80) cc_final: 0.8229 (m-80) REVERT: B 633 TRP cc_start: 0.7923 (p-90) cc_final: 0.7614 (p-90) REVERT: B 699 LEU cc_start: 0.9134 (mm) cc_final: 0.8876 (mm) REVERT: B 1107 ARG cc_start: 0.8042 (mpt-90) cc_final: 0.7805 (mtt180) REVERT: B 1125 ASN cc_start: 0.7542 (t0) cc_final: 0.6828 (t0) outliers start: 175 outliers final: 107 residues processed: 331 average time/residue: 0.3097 time to fit residues: 173.1676 Evaluate side-chains 268 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 149 time to evaluate : 2.675 ------------------------------------------------------------------------------- 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 201 PHE 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 307 THR 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 424 LYS 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 546 LEU 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 874 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 125 ASN 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 201 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 338 PHE 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 551 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 716 THR 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 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL 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 A residue 1141 LEU Chi-restraints excluded: chain B residue 42 VAL 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 201 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL 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 512 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 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1028 LYS 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: 0.7980 chunk 240 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 152 optimal weight: 40.0000 chunk 307 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 409 GLN A 751 ASN B 409 GLN B 751 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091418 restraints weight = 50191.813| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.08 r_work: 0.3122 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 26913 Z= 0.148 Angle : 0.705 18.745 36786 Z= 0.338 Chirality : 0.049 0.471 4332 Planarity : 0.004 0.077 4650 Dihedral : 10.652 88.155 4818 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.79 % Allowed : 22.09 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: -1.66 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 618 sheet: -0.57 (0.20), residues: 603 loop : -2.09 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 633 HIS 0.004 0.001 HIS B 519 PHE 0.015 0.001 PHE A 823 TYR 0.022 0.002 TYR C 170 ARG 0.004 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 42) link_NAG-ASN : angle 3.22227 ( 126) link_BETA1-4 : bond 0.01241 ( 21) link_BETA1-4 : angle 3.91012 ( 63) hydrogen bonds : bond 0.03955 ( 816) hydrogen bonds : angle 5.70104 ( 2238) SS BOND : bond 0.00493 ( 36) SS BOND : angle 2.27063 ( 72) covalent geometry : bond 0.00346 (26814) covalent geometry : angle 0.65412 (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 311 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 176 time to evaluate : 2.874 Fit side-chains revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 265 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.4956 (t80) REVERT: C 266 TYR cc_start: 0.8374 (m-80) cc_final: 0.7969 (m-80) REVERT: C 298 GLU cc_start: 0.8724 (tp30) cc_final: 0.8395 (tp30) REVERT: C 655 TYR cc_start: 0.8670 (t80) cc_final: 0.8053 (t80) REVERT: C 895 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: C 1050 MET cc_start: 0.8938 (ptt) cc_final: 0.8686 (ptp) REVERT: C 1125 ASN cc_start: 0.7607 (t0) cc_final: 0.6730 (t0) REVERT: A 176 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4084 (pt) REVERT: A 265 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.5477 (t80) REVERT: A 298 GLU cc_start: 0.8657 (tp30) cc_final: 0.8397 (tp30) REVERT: A 633 TRP cc_start: 0.8005 (p-90) cc_final: 0.7710 (p-90) REVERT: A 655 TYR cc_start: 0.8655 (t80) cc_final: 0.8216 (t80) REVERT: A 754 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 878 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 1019 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8357 (ttp80) REVERT: A 1125 ASN cc_start: 0.7595 (t0) cc_final: 0.6943 (t0) REVERT: B 229 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6471 (pp) REVERT: B 265 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5269 (t80) REVERT: B 266 TYR cc_start: 0.8349 (m-80) cc_final: 0.8010 (m-80) REVERT: B 633 TRP cc_start: 0.7856 (p-90) cc_final: 0.7528 (p-90) REVERT: B 699 LEU cc_start: 0.9088 (mm) cc_final: 0.8871 (mm) REVERT: B 752 LEU cc_start: 0.9143 (tt) cc_final: 0.8926 (tt) REVERT: B 1125 ASN cc_start: 0.7482 (t0) cc_final: 0.6758 (t0) outliers start: 135 outliers final: 78 residues processed: 284 average time/residue: 0.3103 time to fit residues: 152.3853 Evaluate side-chains 230 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 143 time to evaluate : 2.893 ------------------------------------------------------------------------------- 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 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 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 747 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL 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 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 338 PHE 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 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 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1081 ILE 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 229 LEU Chi-restraints excluded: chain B residue 234 ASN 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 512 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 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 747 THR 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: 0.6980 chunk 80 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 40 optimal weight: 0.0060 chunk 255 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 244 optimal weight: 0.0170 chunk 232 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.3412 ------------------------------------------------------------------------------- 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 895 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 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 = 0.3768 r_free = 0.3768 target = 0.123607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093568 restraints weight = 50060.103| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.08 r_work: 0.3159 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26913 Z= 0.123 Angle : 0.670 19.031 36786 Z= 0.320 Chirality : 0.047 0.464 4332 Planarity : 0.004 0.080 4650 Dihedral : 9.851 84.888 4818 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.33 % Allowed : 22.70 % Favored : 72.98 % 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: -1.55 (0.14), residues: 3234 helix: 1.09 (0.21), residues: 633 sheet: -0.48 (0.20), residues: 573 loop : -2.02 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.003 0.001 HIS B 519 PHE 0.016 0.001 PHE B 168 TYR 0.021 0.001 TYR C 170 ARG 0.004 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 42) link_NAG-ASN : angle 3.16518 ( 126) link_BETA1-4 : bond 0.01240 ( 21) link_BETA1-4 : angle 3.80070 ( 63) hydrogen bonds : bond 0.03655 ( 816) hydrogen bonds : angle 5.50830 ( 2238) SS BOND : bond 0.00466 ( 36) SS BOND : angle 1.76411 ( 72) covalent geometry : bond 0.00272 (26814) covalent geometry : angle 0.62202 (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 301 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 179 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (tt) REVERT: C 265 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.4632 (t80) REVERT: C 266 TYR cc_start: 0.8154 (m-80) cc_final: 0.7926 (m-80) REVERT: C 298 GLU cc_start: 0.8709 (tp30) cc_final: 0.8401 (tp30) REVERT: C 655 TYR cc_start: 0.8635 (t80) cc_final: 0.8087 (t80) REVERT: C 1028 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8858 (mttm) REVERT: C 1050 MET cc_start: 0.8940 (ptt) cc_final: 0.8698 (ptp) REVERT: C 1125 ASN cc_start: 0.7544 (t0) cc_final: 0.6688 (t0) REVERT: A 40 ASP cc_start: 0.7785 (m-30) cc_final: 0.7507 (p0) REVERT: A 265 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5291 (t80) REVERT: A 633 TRP cc_start: 0.7977 (p-90) cc_final: 0.7681 (p-90) REVERT: A 655 TYR cc_start: 0.8628 (t80) cc_final: 0.8414 (t80) REVERT: A 754 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8147 (mp) REVERT: A 1125 ASN cc_start: 0.7423 (t0) cc_final: 0.6716 (t0) REVERT: B 229 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6340 (pp) REVERT: B 265 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.4783 (t80) REVERT: B 266 TYR cc_start: 0.8282 (m-80) cc_final: 0.8058 (m-80) REVERT: B 633 TRP cc_start: 0.7895 (p-90) cc_final: 0.7585 (p-90) REVERT: B 752 LEU cc_start: 0.9125 (tt) cc_final: 0.8834 (tt) REVERT: B 1125 ASN cc_start: 0.7459 (t0) cc_final: 0.6765 (t0) outliers start: 122 outliers final: 78 residues processed: 280 average time/residue: 0.3174 time to fit residues: 151.9820 Evaluate side-chains 236 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 151 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 136 CYS Chi-restraints excluded: chain C residue 201 PHE 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 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 747 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 991 VAL 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 70 VAL Chi-restraints excluded: chain A residue 83 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 131 CYS Chi-restraints excluded: chain A residue 167 THR 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 511 VAL Chi-restraints excluded: chain A residue 512 VAL 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 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 937 SER 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 197 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR 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 511 VAL Chi-restraints excluded: chain B residue 512 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 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR 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: 7.9990 chunk 285 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** 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 = 0.3759 r_free = 0.3759 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092784 restraints weight = 50187.402| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.08 r_work: 0.3150 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26913 Z= 0.136 Angle : 0.665 18.966 36786 Z= 0.316 Chirality : 0.047 0.433 4332 Planarity : 0.004 0.082 4650 Dihedral : 9.204 82.333 4818 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.83 % Allowed : 23.23 % Favored : 72.94 % 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: -1.47 (0.14), residues: 3234 helix: 1.16 (0.21), residues: 633 sheet: -0.45 (0.20), residues: 573 loop : -1.95 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 633 HIS 0.004 0.001 HIS C1088 PHE 0.031 0.001 PHE B 168 TYR 0.020 0.001 TYR C 170 ARG 0.003 0.000 ARG B1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 42) link_NAG-ASN : angle 3.19826 ( 126) link_BETA1-4 : bond 0.01230 ( 21) link_BETA1-4 : angle 3.73931 ( 63) hydrogen bonds : bond 0.03663 ( 816) hydrogen bonds : angle 5.39993 ( 2238) SS BOND : bond 0.00527 ( 36) SS BOND : angle 1.67211 ( 72) covalent geometry : bond 0.00316 (26814) covalent geometry : angle 0.61694 (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 280 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 172 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.6941 (t0) cc_final: 0.6739 (t0) REVERT: C 118 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 265 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4762 (t80) REVERT: C 298 GLU cc_start: 0.8685 (tp30) cc_final: 0.8389 (tp30) REVERT: C 394 ASN cc_start: 0.7621 (t0) cc_final: 0.7370 (t0) REVERT: C 655 TYR cc_start: 0.8664 (t80) cc_final: 0.8092 (t80) REVERT: C 1028 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8933 (mttm) REVERT: C 1050 MET cc_start: 0.8962 (ptt) cc_final: 0.8746 (ptp) REVERT: C 1125 ASN cc_start: 0.7558 (t0) cc_final: 0.6644 (t0) REVERT: A 265 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.5345 (t80) REVERT: A 462 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8586 (mmtm) REVERT: A 633 TRP cc_start: 0.8000 (p-90) cc_final: 0.7770 (p-90) REVERT: A 655 TYR cc_start: 0.8634 (t80) cc_final: 0.8407 (t80) REVERT: A 754 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 1125 ASN cc_start: 0.7305 (t0) cc_final: 0.6551 (t0) REVERT: B 52 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 201 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5825 (m-80) REVERT: B 229 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6343 (pp) REVERT: B 265 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.4523 (t80) REVERT: B 266 TYR cc_start: 0.8317 (m-80) cc_final: 0.8101 (m-80) REVERT: B 633 TRP cc_start: 0.7933 (p-90) cc_final: 0.7588 (p-90) REVERT: B 752 LEU cc_start: 0.9118 (tt) cc_final: 0.8823 (tt) REVERT: B 878 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 1125 ASN cc_start: 0.7508 (t0) cc_final: 0.6749 (t0) outliers start: 108 outliers final: 78 residues processed: 262 average time/residue: 0.2982 time to fit residues: 134.8716 Evaluate side-chains 243 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 156 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 424 LYS 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 590 CYS 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 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 962 LEU 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 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 167 THR 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 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 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET 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 937 SER 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 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 335 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 511 VAL Chi-restraints excluded: chain B residue 512 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 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU 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: 0.0670 chunk 62 optimal weight: 0.4980 chunk 217 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 245 HIS ** 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 = 0.3779 r_free = 0.3779 target = 0.124282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094438 restraints weight = 49830.217| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.08 r_work: 0.3178 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26913 Z= 0.117 Angle : 0.651 18.970 36786 Z= 0.311 Chirality : 0.047 0.426 4332 Planarity : 0.004 0.081 4650 Dihedral : 8.516 79.227 4816 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.55 % Allowed : 23.62 % Favored : 72.84 % 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: -1.42 (0.14), residues: 3234 helix: 1.24 (0.21), residues: 627 sheet: -0.40 (0.21), residues: 573 loop : -1.94 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 633 HIS 0.003 0.001 HIS C1088 PHE 0.022 0.001 PHE B 168 TYR 0.021 0.001 TYR C 170 ARG 0.004 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 42) link_NAG-ASN : angle 3.21162 ( 126) link_BETA1-4 : bond 0.01233 ( 21) link_BETA1-4 : angle 3.69697 ( 63) hydrogen bonds : bond 0.03550 ( 816) hydrogen bonds : angle 5.33546 ( 2238) SS BOND : bond 0.00426 ( 36) SS BOND : angle 1.53106 ( 72) covalent geometry : bond 0.00261 (26814) covalent geometry : angle 0.60306 (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 285 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 185 time to evaluate : 3.086 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: 0.8630 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 266 TYR cc_start: 0.8148 (m-80) cc_final: 0.7942 (m-80) REVERT: C 298 GLU cc_start: 0.8656 (tp30) cc_final: 0.8372 (tp30) REVERT: C 394 ASN cc_start: 0.7587 (t0) cc_final: 0.7348 (t0) REVERT: C 655 TYR cc_start: 0.8640 (t80) cc_final: 0.8108 (t80) REVERT: C 1050 MET cc_start: 0.8936 (ptt) cc_final: 0.8720 (ptp) REVERT: C 1125 ASN cc_start: 0.7623 (t0) cc_final: 0.6704 (t0) REVERT: A 176 LEU cc_start: 0.4568 (OUTLIER) cc_final: 0.4123 (pt) REVERT: A 265 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.5467 (t80) REVERT: A 266 TYR cc_start: 0.8232 (m-80) cc_final: 0.8008 (m-80) REVERT: A 290 ASP cc_start: 0.8401 (t0) cc_final: 0.8114 (m-30) REVERT: A 374 PHE cc_start: 0.6388 (m-10) cc_final: 0.6182 (m-10) REVERT: A 462 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8590 (mmtm) REVERT: A 633 TRP cc_start: 0.7917 (p-90) cc_final: 0.7710 (p-90) REVERT: A 655 TYR cc_start: 0.8614 (t80) cc_final: 0.8409 (t80) REVERT: A 754 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (tt) REVERT: A 1125 ASN cc_start: 0.7319 (t0) cc_final: 0.6561 (t0) REVERT: B 52 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 201 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: B 229 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6269 (pp) REVERT: B 290 ASP cc_start: 0.8297 (t0) cc_final: 0.8044 (m-30) REVERT: B 633 TRP cc_start: 0.8043 (p-90) cc_final: 0.7652 (p-90) REVERT: B 752 LEU cc_start: 0.9104 (tt) cc_final: 0.8893 (tt) REVERT: B 878 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 1125 ASN cc_start: 0.7529 (t0) cc_final: 0.6775 (t0) outliers start: 100 outliers final: 77 residues processed: 262 average time/residue: 0.3229 time to fit residues: 146.9538 Evaluate side-chains 247 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 163 time to evaluate : 2.934 ------------------------------------------------------------------------------- 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 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 424 LYS 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 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 739 THR Chi-restraints excluded: chain C residue 747 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 1122 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 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 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET 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 937 SER 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 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 229 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 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 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS 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 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU 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: 1.9990 chunk 94 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092726 restraints weight = 50418.472| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.09 r_work: 0.3150 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3495 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= 0.139 Angle : 0.657 19.017 36786 Z= 0.313 Chirality : 0.047 0.405 4332 Planarity : 0.004 0.084 4650 Dihedral : 7.950 76.919 4816 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.65 % Allowed : 23.44 % 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: -1.37 (0.14), residues: 3234 helix: 1.32 (0.21), residues: 618 sheet: -0.39 (0.21), residues: 573 loop : -1.90 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 633 HIS 0.003 0.001 HIS B 519 PHE 0.019 0.001 PHE B 643 TYR 0.021 0.001 TYR C 170 ARG 0.006 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 42) link_NAG-ASN : angle 3.22241 ( 126) link_BETA1-4 : bond 0.01194 ( 21) link_BETA1-4 : angle 3.65826 ( 63) hydrogen bonds : bond 0.03664 ( 816) hydrogen bonds : angle 5.33489 ( 2238) SS BOND : bond 0.00618 ( 36) SS BOND : angle 1.90218 ( 72) covalent geometry : bond 0.00320 (26814) covalent geometry : angle 0.60775 (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 266 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 163 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8363 (tt) REVERT: C 298 GLU cc_start: 0.8661 (tp30) cc_final: 0.8362 (tp30) REVERT: C 655 TYR cc_start: 0.8667 (t80) cc_final: 0.8245 (t80) REVERT: C 1050 MET cc_start: 0.8979 (ptt) cc_final: 0.8753 (ptp) REVERT: C 1125 ASN cc_start: 0.7698 (t0) cc_final: 0.6833 (t0) REVERT: A 176 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4175 (pt) REVERT: A 265 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5443 (t80) REVERT: A 290 ASP cc_start: 0.8333 (t0) cc_final: 0.8101 (m-30) REVERT: A 655 TYR cc_start: 0.8649 (t80) cc_final: 0.8424 (t80) REVERT: A 754 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 1125 ASN cc_start: 0.7513 (t0) cc_final: 0.6786 (t0) REVERT: B 52 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 201 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: B 229 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6331 (pp) REVERT: B 633 TRP cc_start: 0.8119 (p-90) cc_final: 0.7801 (p-90) REVERT: B 752 LEU cc_start: 0.9102 (tt) cc_final: 0.8846 (tt) REVERT: B 878 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 1125 ASN cc_start: 0.7519 (t0) cc_final: 0.6737 (t0) outliers start: 103 outliers final: 81 residues processed: 248 average time/residue: 0.3267 time to fit residues: 139.3552 Evaluate side-chains 244 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 156 time to evaluate : 2.885 ------------------------------------------------------------------------------- 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 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 424 LYS 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 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 734 THR Chi-restraints excluded: chain C residue 747 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 991 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 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 590 CYS 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 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 937 SER 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 229 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 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 511 VAL Chi-restraints excluded: chain B residue 512 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 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU 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: 0.0980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 271 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 751 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.122717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092701 restraints weight = 50125.622| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.08 r_work: 0.3149 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26913 Z= 0.138 Angle : 0.653 19.049 36786 Z= 0.312 Chirality : 0.047 0.399 4332 Planarity : 0.004 0.082 4650 Dihedral : 7.473 74.689 4816 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.48 % Allowed : 23.55 % Favored : 72.98 % 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: -1.38 (0.14), residues: 3234 helix: 1.29 (0.21), residues: 618 sheet: -0.40 (0.21), residues: 573 loop : -1.90 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.003 0.001 HIS B 519 PHE 0.018 0.001 PHE B 168 TYR 0.020 0.001 TYR C 170 ARG 0.006 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 42) link_NAG-ASN : angle 3.21566 ( 126) link_BETA1-4 : bond 0.01178 ( 21) link_BETA1-4 : angle 3.64122 ( 63) hydrogen bonds : bond 0.03634 ( 816) hydrogen bonds : angle 5.32977 ( 2238) SS BOND : bond 0.00462 ( 36) SS BOND : angle 1.82498 ( 72) covalent geometry : bond 0.00325 (26814) covalent geometry : angle 0.60322 (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 261 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 163 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8397 (tt) REVERT: C 265 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4870 (t80) REVERT: C 298 GLU cc_start: 0.8657 (tp30) cc_final: 0.8358 (tp30) REVERT: C 655 TYR cc_start: 0.8650 (t80) cc_final: 0.8249 (t80) REVERT: C 1050 MET cc_start: 0.8981 (ptt) cc_final: 0.8757 (ptp) REVERT: C 1125 ASN cc_start: 0.7756 (t0) cc_final: 0.6943 (t0) REVERT: A 176 LEU cc_start: 0.4780 (OUTLIER) cc_final: 0.4308 (pt) REVERT: A 265 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5414 (t80) REVERT: A 290 ASP cc_start: 0.8397 (t0) cc_final: 0.8137 (m-30) REVERT: A 374 PHE cc_start: 0.6282 (m-10) cc_final: 0.5922 (m-10) REVERT: A 462 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8499 (mtmm) REVERT: A 655 TYR cc_start: 0.8639 (t80) cc_final: 0.8406 (t80) REVERT: A 754 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 1028 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8737 (mttm) REVERT: A 1125 ASN cc_start: 0.7546 (t0) cc_final: 0.6829 (t0) REVERT: B 52 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 201 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: B 229 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6312 (pp) REVERT: B 633 TRP cc_start: 0.8053 (p-90) cc_final: 0.7669 (p-90) REVERT: B 752 LEU cc_start: 0.9135 (tt) cc_final: 0.8814 (tt) REVERT: B 878 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8443 (tt) REVERT: B 1125 ASN cc_start: 0.7562 (t0) cc_final: 0.6826 (t0) outliers start: 98 outliers final: 82 residues processed: 243 average time/residue: 0.3156 time to fit residues: 132.2651 Evaluate side-chains 245 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 154 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 424 LYS 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 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 734 THR 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 878 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 991 VAL 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 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 361 CYS 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 590 CYS 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 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 937 SER 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 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 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 511 VAL Chi-restraints excluded: chain B residue 512 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 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 997 ILE 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: 7.9990 chunk 306 optimal weight: 0.0060 chunk 193 optimal weight: 0.0980 chunk 309 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 299 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS C 563 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 239 GLN B 690 GLN B 774 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.124421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094828 restraints weight = 49887.693| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.05 r_work: 0.3184 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26913 Z= 0.111 Angle : 0.638 19.093 36786 Z= 0.304 Chirality : 0.046 0.396 4332 Planarity : 0.004 0.083 4650 Dihedral : 6.956 71.889 4816 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.01 % Allowed : 23.94 % Favored : 73.05 % 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: -1.34 (0.14), residues: 3234 helix: 1.37 (0.21), residues: 621 sheet: -0.43 (0.21), residues: 588 loop : -1.87 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.003 0.001 HIS C1088 PHE 0.018 0.001 PHE B 168 TYR 0.022 0.001 TYR C 170 ARG 0.005 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 42) link_NAG-ASN : angle 3.18770 ( 126) link_BETA1-4 : bond 0.01173 ( 21) link_BETA1-4 : angle 3.60859 ( 63) hydrogen bonds : bond 0.03509 ( 816) hydrogen bonds : angle 5.27619 ( 2238) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.59705 ( 72) covalent geometry : bond 0.00245 (26814) covalent geometry : angle 0.58905 (36525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9993.47 seconds wall clock time: 175 minutes 20.14 seconds (10520.14 seconds total)