Starting phenix.real_space_refine on Sun Jun 22 21:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5r_38073/06_2025/8x5r_38073.cif" } resolution = 3.72 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= 0.052 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 91 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26208 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8442 Classifications: {'peptide': 1086} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.72, per 1000 atoms: 0.60 Number of scatterers: 26208 At special positions: 0 Unit cell: (151, 141, 192, 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 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 657 " " NAG C1305 " - " ASN C 331 " " 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 C1098 " " NAG H 1 " - " ASN C1134 " " NAG I 1 " - " ASN C 343 " " NAG J 1 " - " ASN C 354 " " 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: 7.10 Conformation dependent library (CDL) restraints added in 3.3 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: 54 helices and 50 sheets defined 21.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'C' and resid 69 through 73 removed outlier: 4.010A pdb=" N THR C 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.030A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.457A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.796A 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: 3.683A 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 removed outlier: 3.580A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 941 removed outlier: 4.575A pdb=" N VAL C 915 " --> pdb=" O VAL C 911 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.582A 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: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 removed outlier: 3.999A pdb=" N SER A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.051A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 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: 3.826A 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 869 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 911 through 941 removed outlier: 4.479A pdb=" N VAL A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.604A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.434A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 4.505A pdb=" N THR B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.777A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A 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 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 911 through 941 removed outlier: 4.513A pdb=" N VAL B 915 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.502A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.653A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.468A 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: 7.641A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.858A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.492A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 172 removed outlier: 6.539A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.125A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 removed outlier: 4.308A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.687A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 656 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.772A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'C' and resid 719 through 722 removed outlier: 3.504A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 719 through 722 removed outlier: 7.190A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.678A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.659A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.524A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.044A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.466A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.943A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.432A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 removed outlier: 4.294A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.468A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.681A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 727 removed outlier: 3.565A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.454A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.931A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.575A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.219A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.587A pdb=" N ALA B 397 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.244A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.319A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.489A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.694A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'B' and resid 719 through 727 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'B' and resid 1094 through 1097 809 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.59 Time building geometry restraints manager: 8.33 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: 8240 1.34 - 1.46: 6414 1.46 - 1.59: 12022 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 26814 Sorted by residual: bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.70e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.58e+01 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 34874 1.95 - 3.91: 1473 3.91 - 5.86: 132 5.86 - 7.82: 34 7.82 - 9.77: 12 Bond angle restraints: 36525 Sorted by residual: angle pdb=" N THR B 604 " pdb=" CA THR B 604 " pdb=" C THR B 604 " ideal model delta sigma weight residual 114.62 107.40 7.22 1.14e+00 7.69e-01 4.01e+01 angle pdb=" N VAL C 159 " pdb=" CA VAL C 159 " pdb=" C VAL C 159 " ideal model delta sigma weight residual 113.20 107.29 5.91 9.60e-01 1.09e+00 3.79e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.62 107.96 6.66 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N PHE C 855 " pdb=" CA PHE C 855 " pdb=" C PHE C 855 " ideal model delta sigma weight residual 112.25 104.47 7.78 1.36e+00 5.41e-01 3.27e+01 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 122.65 113.81 8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 14936 23.25 - 46.50: 1383 46.50 - 69.75: 251 69.75 - 92.99: 98 92.99 - 116.24: 105 Dihedral angle restraints: 16773 sinusoidal: 7287 harmonic: 9486 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 171.21 -78.21 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -14.10 -71.90 1 1.00e+01 1.00e-02 6.62e+01 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 35.05 57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 16770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4072 0.106 - 0.212: 243 0.212 - 0.318: 7 0.318 - 0.423: 7 0.423 - 0.529: 3 Chirality restraints: 4332 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.60e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.25e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.12e+01 ... (remaining 4329 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.327 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1307 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " -0.321 2.00e-02 2.50e+03 2.78e-01 9.63e+02 pdb=" C7 NAG C1306 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.134 2.00e-02 2.50e+03 1.14e-01 1.61e+02 pdb=" C7 NAG R 1 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.185 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.105 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2476 2.74 - 3.28: 27807 3.28 - 3.82: 44560 3.82 - 4.36: 51294 4.36 - 4.90: 87493 Nonbonded interactions: 213630 Sorted by model distance: nonbonded pdb=" O GLN B 580 " pdb=" O3 NAG B1305 " model vdw 2.203 3.040 nonbonded pdb=" O VAL B 608 " pdb=" OH TYR B 636 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.208 3.040 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU B 984 " model vdw 2.213 3.120 nonbonded pdb=" O ILE B 805 " pdb=" OG SER B 816 " model vdw 2.225 3.040 ... (remaining 213625 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 61.320 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.094 26913 Z= 0.348 Angle : 0.876 10.563 36786 Z= 0.503 Chirality : 0.056 0.529 4332 Planarity : 0.009 0.285 4650 Dihedral : 20.776 116.242 10569 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.21 % Favored : 90.26 % Rotamer: Outliers : 1.06 % Allowed : 23.58 % Favored : 75.35 % 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: -1.84 (0.14), residues: 3234 helix: 0.71 (0.21), residues: 641 sheet: -0.68 (0.20), residues: 622 loop : -2.20 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 633 HIS 0.004 0.001 HIS A 207 PHE 0.042 0.002 PHE A 201 TYR 0.024 0.002 TYR C 423 ARG 0.007 0.001 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 42) link_NAG-ASN : angle 2.42066 ( 126) link_BETA1-4 : bond 0.01258 ( 21) link_BETA1-4 : angle 4.19122 ( 63) hydrogen bonds : bond 0.20461 ( 805) hydrogen bonds : angle 8.37076 ( 2202) SS BOND : bond 0.00416 ( 36) SS BOND : angle 1.92766 ( 72) covalent geometry : bond 0.00576 (26814) covalent geometry : angle 0.84540 (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 166 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 PRO cc_start: 0.8037 (OUTLIER) cc_final: 0.7055 (Cg_endo) REVERT: C 140 PHE cc_start: 0.7020 (t80) cc_final: 0.6706 (t80) REVERT: C 902 MET cc_start: 0.8824 (tpp) cc_final: 0.8616 (tpt) REVERT: A 835 LYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2328 (pttm) REVERT: A 1030 SER cc_start: 0.8973 (m) cc_final: 0.8152 (m) REVERT: B 1079 PRO cc_start: 0.9141 (Cg_exo) cc_final: 0.8828 (Cg_endo) outliers start: 30 outliers final: 7 residues processed: 160 average time/residue: 0.3621 time to fit residues: 96.3744 Evaluate side-chains 115 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 PRO Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 0.0370 chunk 98 optimal weight: 0.0570 chunk 154 optimal weight: 0.0770 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 overall best weight: 0.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN C 644 GLN C1088 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 901 GLN B 49 HIS B 164 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 644 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.108762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074844 restraints weight = 84323.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077246 restraints weight = 43145.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078791 restraints weight = 28325.833| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26913 Z= 0.145 Angle : 0.744 11.073 36786 Z= 0.355 Chirality : 0.049 0.335 4332 Planarity : 0.005 0.061 4650 Dihedral : 16.354 101.455 4831 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.35 % Favored : 91.31 % Rotamer: Outliers : 2.77 % Allowed : 21.74 % Favored : 75.50 % 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: -1.64 (0.14), residues: 3234 helix: 1.01 (0.21), residues: 641 sheet: -0.43 (0.20), residues: 613 loop : -2.16 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS A1088 PHE 0.023 0.001 PHE C 238 TYR 0.019 0.002 TYR A1067 ARG 0.004 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 42) link_NAG-ASN : angle 2.22705 ( 126) link_BETA1-4 : bond 0.01068 ( 21) link_BETA1-4 : angle 3.68633 ( 63) hydrogen bonds : bond 0.04561 ( 805) hydrogen bonds : angle 6.35292 ( 2202) SS BOND : bond 0.00440 ( 36) SS BOND : angle 1.48664 ( 72) covalent geometry : bond 0.00322 (26814) covalent geometry : angle 0.71563 (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 213 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 135 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 PHE cc_start: 0.6542 (t80) cc_final: 0.6199 (t80) REVERT: C 995 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8599 (ttm170) REVERT: C 1041 ASP cc_start: 0.8140 (t0) cc_final: 0.7425 (t0) REVERT: A 54 LEU cc_start: 0.8258 (mm) cc_final: 0.7606 (tp) REVERT: A 317 ASN cc_start: 0.7736 (m-40) cc_final: 0.7498 (m-40) REVERT: A 423 TYR cc_start: 0.5104 (t80) cc_final: 0.4747 (t80) REVERT: A 434 ILE cc_start: -0.0174 (OUTLIER) cc_final: -0.0414 (mt) REVERT: A 709 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7843 (p0) REVERT: A 835 LYS cc_start: 0.3039 (OUTLIER) cc_final: 0.2227 (pttm) REVERT: A 1030 SER cc_start: 0.9225 (m) cc_final: 0.8775 (m) REVERT: A 1107 ARG cc_start: 0.7744 (mmp-170) cc_final: 0.7280 (tpt90) REVERT: B 409 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 468 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 674 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8427 (t80) outliers start: 78 outliers final: 28 residues processed: 204 average time/residue: 0.3457 time to fit residues: 117.7392 Evaluate side-chains 146 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 1045 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 70 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 311 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 234 optimal weight: 0.2980 chunk 178 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 751 ASN C 853 GLN A 81 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 409 GLN B 895 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.106520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072341 restraints weight = 84167.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074661 restraints weight = 43736.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076160 restraints weight = 28875.335| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26913 Z= 0.198 Angle : 0.733 11.842 36786 Z= 0.349 Chirality : 0.049 0.309 4332 Planarity : 0.004 0.050 4650 Dihedral : 13.665 95.671 4822 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.35 % Favored : 91.34 % Rotamer: Outliers : 3.55 % Allowed : 22.02 % Favored : 74.43 % 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: -1.63 (0.14), residues: 3234 helix: 1.00 (0.21), residues: 642 sheet: -0.65 (0.21), residues: 539 loop : -2.02 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 633 HIS 0.004 0.001 HIS B 245 PHE 0.024 0.002 PHE A 238 TYR 0.018 0.002 TYR B1067 ARG 0.004 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 42) link_NAG-ASN : angle 2.12150 ( 126) link_BETA1-4 : bond 0.01117 ( 21) link_BETA1-4 : angle 3.64288 ( 63) hydrogen bonds : bond 0.04314 ( 805) hydrogen bonds : angle 6.01443 ( 2202) SS BOND : bond 0.00475 ( 36) SS BOND : angle 1.83991 ( 72) covalent geometry : bond 0.00458 (26814) covalent geometry : angle 0.70480 (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 218 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 118 time to evaluate : 5.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.6888 (p) REVERT: C 633 TRP cc_start: 0.4926 (p-90) cc_final: 0.4442 (p-90) REVERT: C 974 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.8853 (t) REVERT: C 995 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8631 (ttp-170) REVERT: A 54 LEU cc_start: 0.8264 (mm) cc_final: 0.7260 (tp) REVERT: A 317 ASN cc_start: 0.7618 (m-40) cc_final: 0.7341 (m-40) REVERT: A 423 TYR cc_start: 0.5313 (t80) cc_final: 0.5033 (t80) REVERT: A 740 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7930 (ttt) REVERT: A 835 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2268 (pttm) REVERT: A 1107 ARG cc_start: 0.7750 (mmp-170) cc_final: 0.7476 (mmm160) REVERT: B 200 TYR cc_start: 0.7720 (m-80) cc_final: 0.7470 (m-80) REVERT: B 916 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (tt) REVERT: B 1041 ASP cc_start: 0.8494 (t70) cc_final: 0.8244 (t70) outliers start: 100 outliers final: 52 residues processed: 208 average time/residue: 0.4557 time to fit residues: 161.1852 Evaluate side-chains 167 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 6.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 2 optimal weight: 0.0470 chunk 44 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.106658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072436 restraints weight = 84783.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074769 restraints weight = 43797.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.076307 restraints weight = 28899.917| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26913 Z= 0.160 Angle : 0.710 11.788 36786 Z= 0.334 Chirality : 0.048 0.269 4332 Planarity : 0.004 0.051 4650 Dihedral : 11.886 89.798 4822 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.19 % Favored : 91.56 % Rotamer: Outliers : 3.51 % Allowed : 22.48 % Favored : 74.01 % 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: -1.58 (0.14), residues: 3234 helix: 1.13 (0.21), residues: 634 sheet: -0.67 (0.22), residues: 533 loop : -1.99 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.001 PHE A 106 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 42) link_NAG-ASN : angle 2.36894 ( 126) link_BETA1-4 : bond 0.01100 ( 21) link_BETA1-4 : angle 3.72762 ( 63) hydrogen bonds : bond 0.03946 ( 805) hydrogen bonds : angle 5.80612 ( 2202) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.59919 ( 72) covalent geometry : bond 0.00366 (26814) covalent geometry : angle 0.67803 (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 222 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 123 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.6813 (p) REVERT: C 115 GLN cc_start: 0.7705 (tt0) cc_final: 0.7414 (tt0) REVERT: C 974 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8838 (t) REVERT: A 317 ASN cc_start: 0.7579 (m-40) cc_final: 0.7346 (m-40) REVERT: A 423 TYR cc_start: 0.5346 (t80) cc_final: 0.5143 (t80) REVERT: A 464 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: A 740 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (ttt) REVERT: A 835 LYS cc_start: 0.3143 (OUTLIER) cc_final: 0.2294 (pttm) REVERT: B 388 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: B 755 GLN cc_start: 0.8839 (pp30) cc_final: 0.8509 (pp30) REVERT: B 1041 ASP cc_start: 0.8430 (t70) cc_final: 0.8142 (t70) outliers start: 99 outliers final: 60 residues processed: 213 average time/residue: 0.4472 time to fit residues: 162.8391 Evaluate side-chains 177 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 111 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 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 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 133 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 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 = 0.3972 r_free = 0.3972 target = 0.104622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071565 restraints weight = 84490.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072926 restraints weight = 53738.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073479 restraints weight = 33922.463| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26913 Z= 0.228 Angle : 0.744 18.160 36786 Z= 0.355 Chirality : 0.048 0.282 4332 Planarity : 0.004 0.052 4650 Dihedral : 10.852 90.324 4818 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.60 % Favored : 91.19 % Rotamer: Outliers : 3.72 % Allowed : 22.84 % Favored : 73.44 % 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: -1.67 (0.14), residues: 3234 helix: 0.84 (0.21), residues: 655 sheet: -0.70 (0.21), residues: 537 loop : -2.01 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 633 HIS 0.003 0.001 HIS B 519 PHE 0.018 0.001 PHE A 106 TYR 0.019 0.002 TYR B 636 ARG 0.005 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 42) link_NAG-ASN : angle 2.37743 ( 126) link_BETA1-4 : bond 0.01078 ( 21) link_BETA1-4 : angle 3.79430 ( 63) hydrogen bonds : bond 0.04139 ( 805) hydrogen bonds : angle 5.82694 ( 2202) SS BOND : bond 0.00573 ( 36) SS BOND : angle 2.90316 ( 72) covalent geometry : bond 0.00528 (26814) covalent geometry : angle 0.70426 (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 225 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 120 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.6899 (p) REVERT: C 115 GLN cc_start: 0.7850 (tt0) cc_final: 0.7576 (tt0) REVERT: C 974 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8932 (t) REVERT: A 131 CYS cc_start: -0.3338 (OUTLIER) cc_final: -0.3611 (t) REVERT: A 166 CYS cc_start: -0.0230 (OUTLIER) cc_final: -0.1413 (t) REVERT: A 317 ASN cc_start: 0.7583 (m-40) cc_final: 0.7346 (m-40) REVERT: A 423 TYR cc_start: 0.5547 (t80) cc_final: 0.5263 (t80) REVERT: A 464 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: A 835 LYS cc_start: 0.3542 (OUTLIER) cc_final: 0.2655 (pttm) REVERT: A 1107 ARG cc_start: 0.7917 (mmp-170) cc_final: 0.7383 (tpt90) REVERT: B 388 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7656 (m110) REVERT: B 674 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 755 GLN cc_start: 0.8891 (pp30) cc_final: 0.8636 (pp30) REVERT: B 756 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8444 (t80) outliers start: 105 outliers final: 72 residues processed: 216 average time/residue: 0.3445 time to fit residues: 124.9595 Evaluate side-chains 186 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 105 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL 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 641 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 247 optimal weight: 6.9990 chunk 80 optimal weight: 0.0070 chunk 191 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 255 optimal weight: 0.7980 chunk 271 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.104175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071023 restraints weight = 83881.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072806 restraints weight = 52060.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073725 restraints weight = 31431.551| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26913 Z= 0.210 Angle : 0.720 12.785 36786 Z= 0.343 Chirality : 0.048 0.288 4332 Planarity : 0.004 0.053 4650 Dihedral : 10.151 83.412 4817 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.63 % Favored : 91.16 % Rotamer: Outliers : 3.94 % Allowed : 23.55 % Favored : 72.52 % 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: -1.69 (0.14), residues: 3234 helix: 0.84 (0.21), residues: 663 sheet: -0.72 (0.21), residues: 530 loop : -2.03 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.003 0.001 HIS B 519 PHE 0.019 0.001 PHE A 106 TYR 0.018 0.002 TYR A1067 ARG 0.005 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 42) link_NAG-ASN : angle 2.14337 ( 126) link_BETA1-4 : bond 0.01081 ( 21) link_BETA1-4 : angle 3.86745 ( 63) hydrogen bonds : bond 0.04065 ( 805) hydrogen bonds : angle 5.75960 ( 2202) SS BOND : bond 0.00445 ( 36) SS BOND : angle 1.95006 ( 72) covalent geometry : bond 0.00486 (26814) covalent geometry : angle 0.68807 (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 225 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 114 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7000 (p) REVERT: A 131 CYS cc_start: -0.3673 (OUTLIER) cc_final: -0.4139 (t) REVERT: A 166 CYS cc_start: 0.0025 (OUTLIER) cc_final: -0.1215 (t) REVERT: A 317 ASN cc_start: 0.7514 (m-40) cc_final: 0.7297 (m-40) REVERT: A 423 TYR cc_start: 0.5575 (t80) cc_final: 0.5339 (t80) REVERT: A 464 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: A 835 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.2623 (pttm) REVERT: A 1107 ARG cc_start: 0.7899 (mmp-170) cc_final: 0.7524 (mmm160) REVERT: B 388 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7671 (m110) REVERT: B 755 GLN cc_start: 0.8873 (pp30) cc_final: 0.8585 (pp30) REVERT: B 756 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8385 (t80) REVERT: B 763 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8691 (tt) outliers start: 111 outliers final: 82 residues processed: 215 average time/residue: 0.3354 time to fit residues: 122.8367 Evaluate side-chains 199 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 109 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 0.0980 chunk 83 optimal weight: 0.0170 chunk 161 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.105700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073287 restraints weight = 84182.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074155 restraints weight = 55951.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074932 restraints weight = 35617.043| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26913 Z= 0.131 Angle : 0.672 13.273 36786 Z= 0.318 Chirality : 0.047 0.284 4332 Planarity : 0.004 0.052 4650 Dihedral : 9.348 80.873 4817 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % Rotamer: Outliers : 3.23 % Allowed : 24.61 % Favored : 72.16 % 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: -1.53 (0.14), residues: 3234 helix: 1.03 (0.21), residues: 655 sheet: -0.54 (0.21), residues: 527 loop : -1.95 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 633 HIS 0.003 0.001 HIS B1088 PHE 0.034 0.001 PHE A 201 TYR 0.017 0.001 TYR C 265 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 42) link_NAG-ASN : angle 1.92979 ( 126) link_BETA1-4 : bond 0.01093 ( 21) link_BETA1-4 : angle 3.84304 ( 63) hydrogen bonds : bond 0.03743 ( 805) hydrogen bonds : angle 5.58627 ( 2202) SS BOND : bond 0.00343 ( 36) SS BOND : angle 1.54365 ( 72) covalent geometry : bond 0.00297 (26814) covalent geometry : angle 0.64208 (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 218 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 498 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7940 (mmp80) REVERT: A 166 CYS cc_start: -0.0490 (OUTLIER) cc_final: -0.1568 (t) REVERT: A 317 ASN cc_start: 0.7608 (m-40) cc_final: 0.7338 (m-40) REVERT: A 456 PHE cc_start: 0.8283 (m-10) cc_final: 0.8070 (m-80) REVERT: A 835 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.2614 (pttm) REVERT: A 1107 ARG cc_start: 0.7919 (mmp-170) cc_final: 0.7522 (mmm160) REVERT: B 388 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7597 (m110) REVERT: B 564 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6026 (tp40) REVERT: B 755 GLN cc_start: 0.8763 (pp30) cc_final: 0.8383 (pp30) REVERT: B 763 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 985 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7802 (m-30) outliers start: 91 outliers final: 62 residues processed: 210 average time/residue: 0.3221 time to fit residues: 115.4771 Evaluate side-chains 174 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 105 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 299 optimal weight: 0.6980 chunk 253 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.105561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072889 restraints weight = 83690.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074203 restraints weight = 51765.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075008 restraints weight = 31685.586| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26913 Z= 0.139 Angle : 0.673 14.068 36786 Z= 0.320 Chirality : 0.046 0.281 4332 Planarity : 0.004 0.053 4650 Dihedral : 8.708 78.385 4816 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.26 % Favored : 91.65 % Rotamer: Outliers : 3.33 % Allowed : 24.68 % Favored : 71.99 % 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: 1.08 (0.21), residues: 648 sheet: -0.57 (0.20), residues: 619 loop : -2.03 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.028 0.001 PHE A 106 TYR 0.015 0.001 TYR A1067 ARG 0.012 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 42) link_NAG-ASN : angle 1.87521 ( 126) link_BETA1-4 : bond 0.01087 ( 21) link_BETA1-4 : angle 3.79814 ( 63) hydrogen bonds : bond 0.03733 ( 805) hydrogen bonds : angle 5.53094 ( 2202) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.68911 ( 72) covalent geometry : bond 0.00322 (26814) covalent geometry : angle 0.64290 (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 210 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 116 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7134 (p) REVERT: C 115 GLN cc_start: 0.8033 (tt0) cc_final: 0.7791 (tt0) REVERT: C 176 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7143 (pt) REVERT: C 498 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.8056 (mmp80) REVERT: C 1050 MET cc_start: 0.8899 (ptm) cc_final: 0.8596 (ptm) REVERT: A 317 ASN cc_start: 0.7584 (m-40) cc_final: 0.7335 (m-40) REVERT: A 456 PHE cc_start: 0.8383 (m-10) cc_final: 0.8115 (m-80) REVERT: A 464 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: A 835 LYS cc_start: 0.3566 (OUTLIER) cc_final: 0.2617 (pttm) REVERT: A 1107 ARG cc_start: 0.7937 (mmp-170) cc_final: 0.7542 (mmm160) REVERT: B 388 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7603 (m110) REVERT: B 755 GLN cc_start: 0.8793 (pp30) cc_final: 0.8399 (pp30) REVERT: B 763 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 967 SER cc_start: 0.8691 (m) cc_final: 0.8196 (p) REVERT: B 985 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7849 (m-30) outliers start: 94 outliers final: 67 residues processed: 200 average time/residue: 0.3705 time to fit residues: 128.1254 Evaluate side-chains 183 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 109 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL 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 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 317 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1054 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 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 = 0.3982 r_free = 0.3982 target = 0.105094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072110 restraints weight = 84266.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.074038 restraints weight = 50607.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074975 restraints weight = 29293.059| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26913 Z= 0.155 Angle : 0.678 14.731 36786 Z= 0.324 Chirality : 0.046 0.281 4332 Planarity : 0.004 0.054 4650 Dihedral : 8.197 75.106 4816 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.43 % Rotamer: Outliers : 3.01 % Allowed : 25.04 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3234 helix: 1.12 (0.21), residues: 640 sheet: -0.45 (0.21), residues: 539 loop : -1.97 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.029 0.001 PHE C 168 TYR 0.017 0.001 TYR B 265 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.83245 ( 126) link_BETA1-4 : bond 0.01078 ( 21) link_BETA1-4 : angle 3.73619 ( 63) hydrogen bonds : bond 0.03794 ( 805) hydrogen bonds : angle 5.54925 ( 2202) SS BOND : bond 0.00346 ( 36) SS BOND : angle 2.16066 ( 72) covalent geometry : bond 0.00358 (26814) covalent geometry : angle 0.64663 (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 201 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 116 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7107 (p) REVERT: C 498 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.8064 (mmp80) REVERT: C 1050 MET cc_start: 0.8919 (ptm) cc_final: 0.8685 (ptm) REVERT: A 317 ASN cc_start: 0.7513 (m-40) cc_final: 0.7309 (m-40) REVERT: A 456 PHE cc_start: 0.8429 (m-10) cc_final: 0.8187 (m-80) REVERT: A 464 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: A 835 LYS cc_start: 0.3530 (OUTLIER) cc_final: 0.2566 (pttm) REVERT: A 1107 ARG cc_start: 0.7959 (mmp-170) cc_final: 0.7569 (mmm160) REVERT: B 388 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7696 (m110) REVERT: B 564 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6097 (tp40) REVERT: B 755 GLN cc_start: 0.8827 (pp30) cc_final: 0.8411 (pp30) REVERT: B 763 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8638 (tt) REVERT: B 967 SER cc_start: 0.8639 (m) cc_final: 0.8127 (p) REVERT: B 985 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7924 (m-30) outliers start: 85 outliers final: 71 residues processed: 192 average time/residue: 0.3532 time to fit residues: 116.0074 Evaluate side-chains 188 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 110 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 290 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 115 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 448 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 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 = 0.3926 r_free = 0.3926 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069541 restraints weight = 84334.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070402 restraints weight = 52096.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070654 restraints weight = 35742.308| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 26913 Z= 0.296 Angle : 0.783 15.239 36786 Z= 0.381 Chirality : 0.050 0.274 4332 Planarity : 0.005 0.058 4650 Dihedral : 8.112 71.515 4816 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.68 % Favored : 90.23 % Rotamer: Outliers : 2.94 % Allowed : 25.28 % Favored : 71.77 % 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: -1.77 (0.14), residues: 3234 helix: 0.54 (0.20), residues: 676 sheet: -0.74 (0.21), residues: 576 loop : -2.04 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS B 49 PHE 0.023 0.002 PHE C 168 TYR 0.024 0.002 TYR B 636 ARG 0.004 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 42) link_NAG-ASN : angle 2.11541 ( 126) link_BETA1-4 : bond 0.01038 ( 21) link_BETA1-4 : angle 3.71162 ( 63) hydrogen bonds : bond 0.04422 ( 805) hydrogen bonds : angle 5.84450 ( 2202) SS BOND : bond 0.00458 ( 36) SS BOND : angle 2.51849 ( 72) covalent geometry : bond 0.00688 (26814) covalent geometry : angle 0.75184 (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 188 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 105 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 902 MET cc_start: 0.9053 (tpp) cc_final: 0.8802 (tpp) REVERT: A 211 ASN cc_start: 0.4388 (OUTLIER) cc_final: 0.2874 (t0) REVERT: A 456 PHE cc_start: 0.8583 (m-10) cc_final: 0.8278 (m-80) REVERT: A 835 LYS cc_start: 0.3796 (OUTLIER) cc_final: 0.2777 (pttm) REVERT: B 388 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7764 (m110) REVERT: B 564 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6139 (tp40) REVERT: B 763 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8770 (tt) REVERT: B 967 SER cc_start: 0.8834 (m) cc_final: 0.8378 (p) REVERT: B 985 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8076 (m-30) outliers start: 83 outliers final: 70 residues processed: 183 average time/residue: 0.3236 time to fit residues: 102.9733 Evaluate side-chains 178 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 102 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 58 optimal weight: 0.9990 chunk 306 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 264 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 299 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN A 52 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.104851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072184 restraints weight = 83373.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073559 restraints weight = 51803.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074572 restraints weight = 31898.412| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26913 Z= 0.132 Angle : 0.683 15.888 36786 Z= 0.326 Chirality : 0.046 0.269 4332 Planarity : 0.004 0.055 4650 Dihedral : 7.603 67.724 4816 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 2.48 % Allowed : 25.53 % Favored : 71.99 % 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: 0.96 (0.21), residues: 645 sheet: -0.61 (0.21), residues: 573 loop : -1.96 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.006 0.001 HIS C1048 PHE 0.026 0.001 PHE C1052 TYR 0.016 0.001 TYR C 265 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 42) link_NAG-ASN : angle 1.87720 ( 126) link_BETA1-4 : bond 0.01037 ( 21) link_BETA1-4 : angle 3.71002 ( 63) hydrogen bonds : bond 0.03851 ( 805) hydrogen bonds : angle 5.60976 ( 2202) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.76589 ( 72) covalent geometry : bond 0.00302 (26814) covalent geometry : angle 0.65361 (36525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8646.87 seconds wall clock time: 155 minutes 0.78 seconds (9300.78 seconds total)