Starting phenix.real_space_refine on Sun Jun 15 09:47:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.map" model { file = "/net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t77_25736/06_2025/7t77_25736.cif" } resolution = 4.75 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= 0.010 sd= 0.100 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 105 5.16 5 C 10473 2.51 5 N 2801 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1077 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.63, per 1000 atoms: 0.57 Number of scatterers: 16832 At special positions: 0 Unit cell: (129.95, 125.35, 165.6, 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 105 16.00 O 3453 8.00 N 2801 7.00 C 10473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.14 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.08 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.16 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA h 3 " - " MAN h 7 " " MAN h 4 " - " MAN h 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 6 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 130 " " NAG A 607 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 185h" " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 448 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 130 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 301 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 448 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN E 130 " " NAG j 1 " - " ASN E 156 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 25 sheets defined 24.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.516A pdb=" N LYS B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.588A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.175A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.733A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.760A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 460 through 464 removed outlier: 4.273A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.740A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.528A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100I through 100M Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.502A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.595A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.758A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 3.745A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AB5, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AB6, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 removed outlier: 5.520A pdb=" N ILE E 215 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY E 250 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR E 217 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'E' and resid 201 through 202 removed outlier: 7.890A pdb=" N GLN E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET E 426 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 302 removed outlier: 7.792A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.812A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 49 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 19 through 24 480 hydrogen bonds defined for protein. 1245 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: 4.74 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 3357 1.32 - 1.47: 6058 1.47 - 1.61: 7591 1.61 - 1.76: 23 1.76 - 1.91: 127 Bond restraints: 17156 Sorted by residual: bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB LEU L 106A" pdb=" CG LEU L 106A" ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NE ARG H 3 " pdb=" CZ ARG H 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.33: 23251 7.33 - 14.65: 41 14.65 - 21.98: 1 21.98 - 29.31: 0 29.31 - 36.63: 3 Bond angle restraints: 23296 Sorted by residual: angle pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " pdb=" C7 NAG A 601 " ideal model delta sigma weight residual 124.56 161.19 -36.63 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C2 NAG E 605 " pdb=" N2 NAG E 605 " pdb=" C7 NAG E 605 " ideal model delta sigma weight residual 124.56 160.59 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 159.61 -35.05 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C HIS E 72 " pdb=" N ALA E 73 " pdb=" CA ALA E 73 " ideal model delta sigma weight residual 122.84 109.29 13.55 1.30e+00 5.92e-01 1.09e+02 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.85 128.36 -8.51 1.01e+00 9.80e-01 7.10e+01 ... (remaining 23291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 11169 21.61 - 43.21: 278 43.21 - 64.82: 86 64.82 - 86.43: 71 86.43 - 108.04: 33 Dihedral angle restraints: 11637 sinusoidal: 5999 harmonic: 5638 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 149.44 -56.44 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 11634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1855 0.107 - 0.214: 642 0.214 - 0.321: 242 0.321 - 0.428: 112 0.428 - 0.535: 62 Chirality restraints: 2913 Sorted by residual: chirality pdb=" C1 MAN R 5 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.36e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.68e+02 ... (remaining 2910 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG i 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG j 2 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.526 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG j 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.210 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4261 2.82 - 3.34: 15821 3.34 - 3.86: 28471 3.86 - 4.38: 34188 4.38 - 4.90: 51974 Nonbonded interactions: 134715 Sorted by model distance: nonbonded pdb=" O TRP E 69 " pdb=" N THR E 71 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS F 574 " model vdw 2.388 3.120 nonbonded pdb=" N GLY A 41 " pdb=" N VAL A 42 " model vdw 2.415 2.560 nonbonded pdb=" N LYS E 97 " pdb=" N ASN E 98 " model vdw 2.418 2.560 nonbonded pdb=" N ASP C 141 " pdb=" OD1 ASP C 141 " model vdw 2.441 3.120 ... (remaining 134710 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 'C' and (resid 32 through 502 or resid 601 through 607)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'i' } ncs_group { reference = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'j' and (resid 1 or resid 4 through 6)) } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.820 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.023 0.136 17295 Z= 1.195 Angle : 1.868 36.634 23679 Z= 1.162 Chirality : 0.153 0.535 2913 Planarity : 0.016 0.304 2833 Dihedral : 13.668 108.037 7897 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.71 % Favored : 97.03 % Rotamer: Outliers : 0.87 % Allowed : 0.93 % Favored : 98.20 % Cbeta Deviations : 0.22 % 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: 0.38 (0.19), residues: 1918 helix: -0.47 (0.23), residues: 417 sheet: 0.70 (0.21), residues: 558 loop : 0.50 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.008 TRP E 479 HIS 0.010 0.002 HIS A 374 PHE 0.045 0.007 PHE C 93 TYR 0.054 0.008 TYR C 40 ARG 0.010 0.001 ARG C 350 Details of bonding type rmsd link_NAG-ASN : bond 0.07869 ( 60) link_NAG-ASN : angle 2.59678 ( 180) link_ALPHA1-6 : bond 0.03867 ( 4) link_ALPHA1-6 : angle 5.07501 ( 12) link_BETA1-4 : bond 0.06823 ( 36) link_BETA1-4 : angle 4.88253 ( 108) link_ALPHA1-3 : bond 0.03632 ( 5) link_ALPHA1-3 : angle 2.17157 ( 15) hydrogen bonds : bond 0.15932 ( 480) hydrogen bonds : angle 7.88011 ( 1245) SS BOND : bond 0.03725 ( 34) SS BOND : angle 3.00027 ( 68) covalent geometry : bond 0.02187 (17156) covalent geometry : angle 1.82781 (23296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9519 (mt) cc_final: 0.9049 (tp) REVERT: A 180 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (m-30) REVERT: A 271 ILE cc_start: 0.9434 (mt) cc_final: 0.9209 (tp) REVERT: A 423 ILE cc_start: 0.9118 (mt) cc_final: 0.8755 (mm) REVERT: B 528 SER cc_start: 0.8591 (m) cc_final: 0.7830 (t) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8383 (mtm) REVERT: B 584 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8939 (tp30) REVERT: B 647 GLU cc_start: 0.8993 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 651 ASN cc_start: 0.8977 (m-40) cc_final: 0.8690 (p0) REVERT: B 654 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7934 (tm-30) REVERT: C 53 PHE cc_start: 0.7879 (m-80) cc_final: 0.7627 (m-10) REVERT: C 101 VAL cc_start: 0.9492 (t) cc_final: 0.9286 (p) REVERT: C 383 PHE cc_start: 0.9129 (m-80) cc_final: 0.8804 (m-80) REVERT: C 384 TYR cc_start: 0.8917 (m-80) cc_final: 0.8440 (m-80) REVERT: C 424 ILE cc_start: 0.8785 (mt) cc_final: 0.8583 (mm) REVERT: D 536 THR cc_start: 0.9269 (p) cc_final: 0.8962 (t) REVERT: D 538 THR cc_start: 0.9005 (p) cc_final: 0.7872 (p) REVERT: D 650 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7904 (tp40) REVERT: E 42 VAL cc_start: 0.9085 (t) cc_final: 0.8673 (t) REVERT: E 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8294 (m-90) REVERT: E 87 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8431 (t0) REVERT: E 254 VAL cc_start: 0.9475 (t) cc_final: 0.9233 (p) REVERT: F 530 MET cc_start: 0.9365 (mtp) cc_final: 0.9047 (mtp) REVERT: F 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8619 (tpp) REVERT: F 540 GLN cc_start: 0.8731 (mm110) cc_final: 0.8004 (mt0) REVERT: F 573 ILE cc_start: 0.8643 (mt) cc_final: 0.8334 (mm) REVERT: F 574 LYS cc_start: 0.8958 (mttt) cc_final: 0.8475 (mtmt) REVERT: F 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8871 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9346 (mmmt) REVERT: F 643 TYR cc_start: 0.9363 (m-10) cc_final: 0.9009 (m-80) REVERT: F 648 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8551 (tt0) REVERT: F 660 LEU cc_start: 0.8323 (mt) cc_final: 0.8029 (mt) REVERT: H 28 ASP cc_start: 0.8808 (t0) cc_final: 0.8297 (t0) REVERT: H 67 LEU cc_start: 0.8266 (mt) cc_final: 0.8016 (mm) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9046 (tp) REVERT: H 82 MET cc_start: 0.9002 (ptp) cc_final: 0.8520 (ttt) REVERT: H 91 PHE cc_start: 0.9263 (m-80) cc_final: 0.8933 (m-80) REVERT: L 4 LEU cc_start: 0.8996 (mt) cc_final: 0.8675 (tt) REVERT: L 36 TYR cc_start: 0.8280 (m-80) cc_final: 0.7911 (m-80) REVERT: L 69 ASN cc_start: 0.8219 (m-40) cc_final: 0.7683 (m-40) REVERT: L 78 LEU cc_start: 0.8730 (tp) cc_final: 0.8527 (tt) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7463 (m-30) REVERT: L 88 CYS cc_start: 0.3702 (p) cc_final: 0.3100 (p) REVERT: L 96 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8662 (mmt90) outliers start: 15 outliers final: 6 residues processed: 406 average time/residue: 0.3056 time to fit residues: 181.3346 Evaluate side-chains 207 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.0170 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 HIS B 652 GLN B 658 GLN C 66 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 136 ASN E 195 ASN F 543 ASN L 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044473 restraints weight = 92621.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.046324 restraints weight = 54122.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047676 restraints weight = 36975.377| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17295 Z= 0.178 Angle : 0.859 16.770 23679 Z= 0.408 Chirality : 0.050 0.386 2913 Planarity : 0.004 0.047 2833 Dihedral : 11.210 81.112 4264 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.35 % Allowed : 1.69 % Favored : 97.97 % 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: 0.32 (0.19), residues: 1918 helix: 1.01 (0.26), residues: 372 sheet: 0.32 (0.20), residues: 597 loop : -0.06 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.012 0.001 HIS A 190 PHE 0.025 0.002 PHE A 233 TYR 0.038 0.002 TYR C 484 ARG 0.007 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 60) link_NAG-ASN : angle 3.24726 ( 180) link_ALPHA1-6 : bond 0.01864 ( 4) link_ALPHA1-6 : angle 3.15019 ( 12) link_BETA1-4 : bond 0.00721 ( 36) link_BETA1-4 : angle 3.27530 ( 108) link_ALPHA1-3 : bond 0.00846 ( 5) link_ALPHA1-3 : angle 2.18778 ( 15) hydrogen bonds : bond 0.05558 ( 480) hydrogen bonds : angle 6.32301 ( 1245) SS BOND : bond 0.00432 ( 34) SS BOND : angle 1.26700 ( 68) covalent geometry : bond 0.00390 (17156) covalent geometry : angle 0.77832 (23296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.9053 (m-30) cc_final: 0.8292 (m-30) REVERT: A 201 ILE cc_start: 0.9266 (mp) cc_final: 0.8447 (tp) REVERT: A 271 ILE cc_start: 0.9238 (mt) cc_final: 0.8960 (tp) REVERT: A 423 ILE cc_start: 0.9034 (mt) cc_final: 0.8576 (mm) REVERT: A 425 ASN cc_start: 0.8466 (p0) cc_final: 0.8117 (p0) REVERT: A 491 ILE cc_start: 0.9072 (tp) cc_final: 0.8708 (tp) REVERT: A 492 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8200 (mp0) REVERT: A 494 LEU cc_start: 0.8330 (mt) cc_final: 0.7848 (mt) REVERT: B 528 SER cc_start: 0.8473 (m) cc_final: 0.7794 (t) REVERT: B 574 LYS cc_start: 0.8964 (pptt) cc_final: 0.8754 (tmtt) REVERT: B 647 GLU cc_start: 0.9055 (tt0) cc_final: 0.8709 (tm-30) REVERT: B 648 GLU cc_start: 0.9199 (tp30) cc_final: 0.8922 (tp30) REVERT: C 150 MET cc_start: 0.8727 (mmt) cc_final: 0.8494 (mmm) REVERT: C 186 ARG cc_start: 0.8116 (mmp80) cc_final: 0.7198 (ptm160) REVERT: C 217 TYR cc_start: 0.7380 (m-10) cc_final: 0.7053 (m-10) REVERT: C 489 VAL cc_start: 0.8940 (m) cc_final: 0.8713 (t) REVERT: D 536 THR cc_start: 0.9012 (p) cc_final: 0.8776 (t) REVERT: D 538 THR cc_start: 0.8586 (p) cc_final: 0.8089 (t) REVERT: D 584 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8872 (tp30) REVERT: D 650 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7682 (tp-100) REVERT: D 653 GLN cc_start: 0.9041 (pp30) cc_final: 0.8811 (pp30) REVERT: E 42 VAL cc_start: 0.8706 (t) cc_final: 0.8475 (t) REVERT: E 69 TRP cc_start: 0.8700 (m-90) cc_final: 0.8160 (m-10) REVERT: E 98 ASN cc_start: 0.9190 (t0) cc_final: 0.7887 (t0) REVERT: E 434 MET cc_start: 0.8661 (mtp) cc_final: 0.8447 (mtp) REVERT: E 475 MET cc_start: 0.7515 (mtp) cc_final: 0.6930 (mtp) REVERT: F 530 MET cc_start: 0.9108 (mtp) cc_final: 0.8674 (mtp) REVERT: F 535 MET cc_start: 0.8775 (mmp) cc_final: 0.8409 (tpp) REVERT: F 536 THR cc_start: 0.9254 (t) cc_final: 0.9020 (p) REVERT: F 633 LYS cc_start: 0.9702 (mttt) cc_final: 0.9306 (mmmt) REVERT: H 12 VAL cc_start: 0.8432 (m) cc_final: 0.8063 (m) REVERT: H 28 ASP cc_start: 0.8779 (t0) cc_final: 0.8471 (t70) REVERT: H 45 LEU cc_start: 0.9300 (mm) cc_final: 0.8925 (mm) REVERT: H 78 LEU cc_start: 0.9421 (tp) cc_final: 0.9111 (tp) REVERT: H 82 MET cc_start: 0.9162 (ptp) cc_final: 0.8885 (ttt) REVERT: H 82 ASN cc_start: 0.8203 (m-40) cc_final: 0.7915 (p0) REVERT: H 100 MET cc_start: 0.9279 (mpp) cc_final: 0.8933 (mpp) REVERT: L 36 TYR cc_start: 0.8348 (m-80) cc_final: 0.6741 (m-80) REVERT: L 50 ASP cc_start: 0.8045 (m-30) cc_final: 0.7414 (m-30) REVERT: L 69 ASN cc_start: 0.8350 (m-40) cc_final: 0.7663 (m-40) REVERT: L 86 TYR cc_start: 0.8611 (m-80) cc_final: 0.7949 (m-80) REVERT: L 89 LYS cc_start: 0.9278 (ttpp) cc_final: 0.8948 (ttpt) REVERT: L 104 LEU cc_start: 0.8899 (tt) cc_final: 0.8446 (tt) outliers start: 6 outliers final: 2 residues processed: 267 average time/residue: 0.2497 time to fit residues: 104.2584 Evaluate side-chains 180 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 40 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 38 optimal weight: 0.0040 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 625 ASN D 651 ASN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044167 restraints weight = 92055.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.046035 restraints weight = 53089.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047387 restraints weight = 35931.904| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17295 Z= 0.134 Angle : 0.717 9.642 23679 Z= 0.339 Chirality : 0.047 0.351 2913 Planarity : 0.004 0.044 2833 Dihedral : 9.151 74.569 4264 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.19), residues: 1918 helix: 0.93 (0.27), residues: 372 sheet: 0.25 (0.21), residues: 565 loop : -0.11 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.007 0.001 HIS A 190 PHE 0.018 0.001 PHE H 100J TYR 0.023 0.002 TYR D 643 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 60) link_NAG-ASN : angle 2.67491 ( 180) link_ALPHA1-6 : bond 0.01668 ( 4) link_ALPHA1-6 : angle 2.55514 ( 12) link_BETA1-4 : bond 0.00718 ( 36) link_BETA1-4 : angle 2.78875 ( 108) link_ALPHA1-3 : bond 0.00923 ( 5) link_ALPHA1-3 : angle 1.80342 ( 15) hydrogen bonds : bond 0.04581 ( 480) hydrogen bonds : angle 5.95753 ( 1245) SS BOND : bond 0.00420 ( 34) SS BOND : angle 1.21333 ( 68) covalent geometry : bond 0.00283 (17156) covalent geometry : angle 0.64906 (23296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.9366 (t0) cc_final: 0.9045 (t0) REVERT: A 180 ASP cc_start: 0.9037 (m-30) cc_final: 0.8236 (m-30) REVERT: A 201 ILE cc_start: 0.9347 (mp) cc_final: 0.8602 (tp) REVERT: A 271 ILE cc_start: 0.9256 (mt) cc_final: 0.9002 (tp) REVERT: A 359 ILE cc_start: 0.8749 (mm) cc_final: 0.8437 (mm) REVERT: A 423 ILE cc_start: 0.8977 (mt) cc_final: 0.8567 (mm) REVERT: A 425 ASN cc_start: 0.8336 (p0) cc_final: 0.8029 (p0) REVERT: A 434 MET cc_start: 0.8690 (tpp) cc_final: 0.8422 (tpp) REVERT: A 491 ILE cc_start: 0.8949 (tp) cc_final: 0.8738 (tp) REVERT: A 494 LEU cc_start: 0.8300 (mt) cc_final: 0.7914 (mt) REVERT: B 528 SER cc_start: 0.8596 (m) cc_final: 0.7886 (t) REVERT: B 574 LYS cc_start: 0.8983 (pptt) cc_final: 0.8724 (tmtt) REVERT: B 626 MET cc_start: 0.8468 (mmp) cc_final: 0.7926 (mmm) REVERT: B 633 LYS cc_start: 0.9630 (mtmm) cc_final: 0.9420 (mtmm) REVERT: B 647 GLU cc_start: 0.9419 (tt0) cc_final: 0.8937 (tm-30) REVERT: B 648 GLU cc_start: 0.9257 (tp30) cc_final: 0.8914 (tp30) REVERT: B 651 ASN cc_start: 0.8970 (p0) cc_final: 0.8693 (p0) REVERT: B 657 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8598 (mt-10) REVERT: C 186 ARG cc_start: 0.8197 (mmp80) cc_final: 0.7183 (ptm160) REVERT: D 536 THR cc_start: 0.8847 (p) cc_final: 0.8632 (t) REVERT: D 584 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8899 (tp30) REVERT: D 601 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8721 (ptpp) REVERT: D 626 MET cc_start: 0.9038 (tpp) cc_final: 0.8805 (tpp) REVERT: D 642 ILE cc_start: 0.9152 (tt) cc_final: 0.8783 (tt) REVERT: D 646 LEU cc_start: 0.9659 (mt) cc_final: 0.9442 (mt) REVERT: D 658 GLN cc_start: 0.8421 (mt0) cc_final: 0.8119 (mt0) REVERT: E 42 VAL cc_start: 0.8683 (t) cc_final: 0.8446 (t) REVERT: E 69 TRP cc_start: 0.8669 (m-90) cc_final: 0.8243 (m-10) REVERT: E 98 ASN cc_start: 0.9234 (t0) cc_final: 0.8514 (t0) REVERT: F 535 MET cc_start: 0.8725 (mmp) cc_final: 0.8429 (tpp) REVERT: F 633 LYS cc_start: 0.9676 (mttt) cc_final: 0.9296 (mmmt) REVERT: H 28 ASP cc_start: 0.8831 (t0) cc_final: 0.8450 (t70) REVERT: H 45 LEU cc_start: 0.9356 (mm) cc_final: 0.8959 (mm) REVERT: H 78 LEU cc_start: 0.9470 (tp) cc_final: 0.9160 (tp) REVERT: H 82 MET cc_start: 0.9200 (ptp) cc_final: 0.8942 (tpt) REVERT: H 100 MET cc_start: 0.9160 (mpp) cc_final: 0.8824 (mpp) REVERT: L 36 TYR cc_start: 0.8419 (m-80) cc_final: 0.7446 (m-80) REVERT: L 86 TYR cc_start: 0.8652 (m-80) cc_final: 0.7914 (m-80) REVERT: L 104 LEU cc_start: 0.9035 (tt) cc_final: 0.8475 (tt) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.2564 time to fit residues: 94.9090 Evaluate side-chains 173 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 543 ASN D 585 HIS D 607 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS H 100RHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.037897 restraints weight = 100301.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.039452 restraints weight = 60710.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040587 restraints weight = 42810.959| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17295 Z= 0.326 Angle : 0.945 11.273 23679 Z= 0.452 Chirality : 0.050 0.385 2913 Planarity : 0.006 0.063 2833 Dihedral : 8.301 71.793 4264 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -0.45 (0.19), residues: 1918 helix: 0.46 (0.26), residues: 360 sheet: -0.31 (0.21), residues: 552 loop : -0.48 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 596 HIS 0.011 0.002 HIS C 85 PHE 0.022 0.003 PHE A 391 TYR 0.028 0.003 TYR F 586 ARG 0.007 0.001 ARG E 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 60) link_NAG-ASN : angle 2.92059 ( 180) link_ALPHA1-6 : bond 0.01407 ( 4) link_ALPHA1-6 : angle 2.92166 ( 12) link_BETA1-4 : bond 0.00619 ( 36) link_BETA1-4 : angle 2.83086 ( 108) link_ALPHA1-3 : bond 0.00694 ( 5) link_ALPHA1-3 : angle 2.12292 ( 15) hydrogen bonds : bond 0.04939 ( 480) hydrogen bonds : angle 6.20565 ( 1245) SS BOND : bond 0.00455 ( 34) SS BOND : angle 1.45017 ( 68) covalent geometry : bond 0.00680 (17156) covalent geometry : angle 0.88923 (23296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8412 (m-10) cc_final: 0.8125 (m-10) REVERT: A 98 ASN cc_start: 0.9376 (t0) cc_final: 0.9065 (t0) REVERT: A 201 ILE cc_start: 0.9454 (mp) cc_final: 0.8851 (tp) REVERT: A 260 LEU cc_start: 0.9455 (mp) cc_final: 0.9244 (mp) REVERT: A 425 ASN cc_start: 0.8364 (p0) cc_final: 0.7912 (p0) REVERT: B 536 THR cc_start: 0.9044 (m) cc_final: 0.8828 (p) REVERT: B 626 MET cc_start: 0.8705 (mmp) cc_final: 0.8009 (mmm) REVERT: B 638 TYR cc_start: 0.8116 (t80) cc_final: 0.7719 (t80) REVERT: B 647 GLU cc_start: 0.9418 (tt0) cc_final: 0.8678 (mm-30) REVERT: B 648 GLU cc_start: 0.9140 (tp30) cc_final: 0.8892 (tp30) REVERT: B 651 ASN cc_start: 0.9251 (p0) cc_final: 0.8889 (p0) REVERT: C 186 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7022 (ptm160) REVERT: D 601 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8904 (mtpt) REVERT: E 98 ASN cc_start: 0.9416 (t0) cc_final: 0.9045 (t0) REVERT: E 434 MET cc_start: 0.8929 (mtp) cc_final: 0.8553 (mtp) REVERT: E 453 ILE cc_start: 0.8733 (mm) cc_final: 0.8438 (tp) REVERT: E 478 ASN cc_start: 0.9012 (t0) cc_final: 0.8736 (t0) REVERT: F 530 MET cc_start: 0.9238 (mtp) cc_final: 0.8830 (mtp) REVERT: F 535 MET cc_start: 0.8788 (mmp) cc_final: 0.8455 (tpp) REVERT: F 570 HIS cc_start: 0.7084 (p-80) cc_final: 0.6627 (p90) REVERT: F 601 LYS cc_start: 0.9482 (mttt) cc_final: 0.8786 (mtmt) REVERT: F 633 LYS cc_start: 0.9679 (mttt) cc_final: 0.9352 (mmmt) REVERT: F 650 GLN cc_start: 0.7423 (tp40) cc_final: 0.6678 (tp40) REVERT: F 655 LYS cc_start: 0.9593 (ttmm) cc_final: 0.8952 (ttmm) REVERT: H 45 LEU cc_start: 0.9569 (mm) cc_final: 0.9262 (mm) REVERT: H 78 LEU cc_start: 0.9444 (tp) cc_final: 0.9189 (tp) REVERT: H 82 MET cc_start: 0.9391 (ptp) cc_final: 0.9115 (tpp) REVERT: H 82 LEU cc_start: 0.9376 (mt) cc_final: 0.8721 (mt) REVERT: H 100 MET cc_start: 0.9295 (mpp) cc_final: 0.8898 (mpp) REVERT: L 6 GLN cc_start: 0.6755 (mt0) cc_final: 0.6530 (mt0) REVERT: L 35 TRP cc_start: 0.8193 (m100) cc_final: 0.7740 (m100) REVERT: L 88 CYS cc_start: 0.3155 (p) cc_final: 0.2880 (p) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2837 time to fit residues: 74.9153 Evaluate side-chains 127 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.039426 restraints weight = 98174.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.041089 restraints weight = 57802.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042301 restraints weight = 40054.890| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17295 Z= 0.146 Angle : 0.678 13.312 23679 Z= 0.328 Chirality : 0.046 0.292 2913 Planarity : 0.004 0.080 2833 Dihedral : 7.508 65.686 4264 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.19), residues: 1918 helix: 0.65 (0.27), residues: 381 sheet: -0.08 (0.22), residues: 540 loop : -0.41 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 35 HIS 0.007 0.001 HIS A 249 PHE 0.012 0.001 PHE E 382 TYR 0.029 0.002 TYR F 586 ARG 0.016 0.001 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 60) link_NAG-ASN : angle 2.32706 ( 180) link_ALPHA1-6 : bond 0.01575 ( 4) link_ALPHA1-6 : angle 2.47874 ( 12) link_BETA1-4 : bond 0.00538 ( 36) link_BETA1-4 : angle 2.33242 ( 108) link_ALPHA1-3 : bond 0.00920 ( 5) link_ALPHA1-3 : angle 1.88098 ( 15) hydrogen bonds : bond 0.04061 ( 480) hydrogen bonds : angle 5.56468 ( 1245) SS BOND : bond 0.00310 ( 34) SS BOND : angle 1.17615 ( 68) covalent geometry : bond 0.00319 (17156) covalent geometry : angle 0.62495 (23296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8346 (m-10) cc_final: 0.8066 (m-10) REVERT: A 98 ASN cc_start: 0.9357 (t0) cc_final: 0.8970 (t0) REVERT: A 201 ILE cc_start: 0.9446 (mp) cc_final: 0.8851 (tp) REVERT: A 425 ASN cc_start: 0.8207 (p0) cc_final: 0.7793 (p0) REVERT: A 494 LEU cc_start: 0.8790 (mt) cc_final: 0.7988 (mt) REVERT: B 638 TYR cc_start: 0.7971 (t80) cc_final: 0.7765 (t80) REVERT: B 655 LYS cc_start: 0.9395 (pttp) cc_final: 0.9026 (pptt) REVERT: C 150 MET cc_start: 0.8825 (mmp) cc_final: 0.8561 (mmt) REVERT: C 186 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7112 (ptm160) REVERT: D 584 GLU cc_start: 0.9293 (tt0) cc_final: 0.8873 (tp30) REVERT: E 69 TRP cc_start: 0.8726 (m-90) cc_final: 0.8297 (m-90) REVERT: E 98 ASN cc_start: 0.9365 (t0) cc_final: 0.9093 (t0) REVERT: E 434 MET cc_start: 0.8834 (mtp) cc_final: 0.8465 (mtp) REVERT: E 453 ILE cc_start: 0.8575 (mm) cc_final: 0.8187 (tp) REVERT: E 478 ASN cc_start: 0.9038 (t0) cc_final: 0.8807 (t0) REVERT: F 530 MET cc_start: 0.9157 (mtp) cc_final: 0.8724 (mtp) REVERT: F 570 HIS cc_start: 0.7079 (p-80) cc_final: 0.6623 (p90) REVERT: F 601 LYS cc_start: 0.9376 (mttt) cc_final: 0.8925 (mtmt) REVERT: F 633 LYS cc_start: 0.9679 (mttt) cc_final: 0.9334 (mmmt) REVERT: F 650 GLN cc_start: 0.7133 (tp40) cc_final: 0.6417 (tp40) REVERT: H 45 LEU cc_start: 0.9498 (mm) cc_final: 0.9265 (mm) REVERT: H 76 ASP cc_start: 0.8044 (m-30) cc_final: 0.7675 (t0) REVERT: H 78 LEU cc_start: 0.9488 (tp) cc_final: 0.9262 (tp) REVERT: H 82 MET cc_start: 0.9384 (ptp) cc_final: 0.9099 (tpt) REVERT: H 82 LEU cc_start: 0.9391 (mt) cc_final: 0.8652 (mt) REVERT: L 35 TRP cc_start: 0.8270 (m100) cc_final: 0.7859 (m100) REVERT: L 88 CYS cc_start: 0.3126 (p) cc_final: 0.2860 (p) REVERT: L 89 LYS cc_start: 0.9408 (ttpp) cc_final: 0.8953 (tmmt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2691 time to fit residues: 76.0036 Evaluate side-chains 132 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.036578 restraints weight = 100783.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.038079 restraints weight = 60359.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.039156 restraints weight = 42436.265| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 17295 Z= 0.299 Angle : 0.864 12.208 23679 Z= 0.418 Chirality : 0.049 0.324 2913 Planarity : 0.006 0.197 2833 Dihedral : 7.855 64.949 4264 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.19), residues: 1918 helix: 0.18 (0.26), residues: 378 sheet: -0.47 (0.22), residues: 548 loop : -0.72 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 479 HIS 0.013 0.002 HIS E 374 PHE 0.018 0.003 PHE E 382 TYR 0.030 0.003 TYR F 586 ARG 0.009 0.001 ARG E 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 60) link_NAG-ASN : angle 2.51318 ( 180) link_ALPHA1-6 : bond 0.01502 ( 4) link_ALPHA1-6 : angle 2.35431 ( 12) link_BETA1-4 : bond 0.00667 ( 36) link_BETA1-4 : angle 2.56614 ( 108) link_ALPHA1-3 : bond 0.00677 ( 5) link_ALPHA1-3 : angle 2.17282 ( 15) hydrogen bonds : bond 0.04592 ( 480) hydrogen bonds : angle 5.98542 ( 1245) SS BOND : bond 0.00795 ( 34) SS BOND : angle 1.41273 ( 68) covalent geometry : bond 0.00624 (17156) covalent geometry : angle 0.81723 (23296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8520 (m-10) cc_final: 0.8285 (m-10) REVERT: A 201 ILE cc_start: 0.9488 (mp) cc_final: 0.8924 (tp) REVERT: A 425 ASN cc_start: 0.8141 (p0) cc_final: 0.7628 (p0) REVERT: B 528 SER cc_start: 0.9327 (m) cc_final: 0.8662 (p) REVERT: B 530 MET cc_start: 0.8613 (tpp) cc_final: 0.8386 (tpp) REVERT: B 536 THR cc_start: 0.9126 (m) cc_final: 0.8875 (p) REVERT: B 601 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8327 (mmmm) REVERT: B 626 MET cc_start: 0.8568 (mmp) cc_final: 0.8055 (mmm) REVERT: B 648 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8916 (tm-30) REVERT: B 655 LYS cc_start: 0.9340 (pttp) cc_final: 0.9024 (pptt) REVERT: C 100 MET cc_start: 0.8672 (mmm) cc_final: 0.8362 (tpt) REVERT: C 150 MET cc_start: 0.8989 (mmp) cc_final: 0.8636 (mmt) REVERT: C 186 ARG cc_start: 0.8291 (mmp80) cc_final: 0.7337 (ptm160) REVERT: D 584 GLU cc_start: 0.9320 (tt0) cc_final: 0.9001 (tp30) REVERT: D 610 TRP cc_start: 0.7272 (p90) cc_final: 0.6702 (p90) REVERT: D 626 MET cc_start: 0.9524 (mmp) cc_final: 0.9097 (tpp) REVERT: D 650 GLN cc_start: 0.8696 (tp-100) cc_final: 0.7723 (tp-100) REVERT: E 69 TRP cc_start: 0.8943 (m-90) cc_final: 0.8357 (m-90) REVERT: E 100 MET cc_start: 0.9441 (mtm) cc_final: 0.9237 (mtp) REVERT: E 279 ASN cc_start: 0.8929 (t0) cc_final: 0.8287 (t0) REVERT: E 453 ILE cc_start: 0.8774 (mm) cc_final: 0.8487 (tp) REVERT: E 478 ASN cc_start: 0.9068 (t0) cc_final: 0.8847 (t0) REVERT: F 530 MET cc_start: 0.8996 (mtp) cc_final: 0.8241 (ttp) REVERT: F 570 HIS cc_start: 0.7200 (p-80) cc_final: 0.6990 (p90) REVERT: F 633 LYS cc_start: 0.9701 (mttt) cc_final: 0.9359 (mmmt) REVERT: F 650 GLN cc_start: 0.7553 (tp40) cc_final: 0.6742 (tp40) REVERT: F 655 LYS cc_start: 0.9622 (ttmm) cc_final: 0.8929 (ttmm) REVERT: H 45 LEU cc_start: 0.9544 (mm) cc_final: 0.9273 (mm) REVERT: H 75 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9199 (mtmt) REVERT: H 78 LEU cc_start: 0.9470 (tp) cc_final: 0.9245 (tp) REVERT: H 82 MET cc_start: 0.9551 (ptp) cc_final: 0.9099 (tpt) REVERT: L 35 TRP cc_start: 0.8203 (m100) cc_final: 0.7186 (m100) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2514 time to fit residues: 63.8327 Evaluate side-chains 121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 0.0270 chunk 33 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.038605 restraints weight = 99157.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.040158 restraints weight = 59859.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.041267 restraints weight = 42295.338| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17295 Z= 0.139 Angle : 0.667 13.703 23679 Z= 0.326 Chirality : 0.046 0.263 2913 Planarity : 0.005 0.157 2833 Dihedral : 7.299 59.548 4264 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.53 (0.19), residues: 1918 helix: 0.45 (0.27), residues: 384 sheet: -0.28 (0.22), residues: 544 loop : -0.63 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 112 HIS 0.007 0.001 HIS H 35 PHE 0.013 0.001 PHE E 382 TYR 0.015 0.002 TYR C 191 ARG 0.016 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 60) link_NAG-ASN : angle 2.33135 ( 180) link_ALPHA1-6 : bond 0.01265 ( 4) link_ALPHA1-6 : angle 1.81559 ( 12) link_BETA1-4 : bond 0.00488 ( 36) link_BETA1-4 : angle 2.20778 ( 108) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 2.09076 ( 15) hydrogen bonds : bond 0.03985 ( 480) hydrogen bonds : angle 5.46626 ( 1245) SS BOND : bond 0.00428 ( 34) SS BOND : angle 1.16388 ( 68) covalent geometry : bond 0.00297 (17156) covalent geometry : angle 0.61528 (23296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8480 (ptp) cc_final: 0.8212 (ptt) REVERT: A 201 ILE cc_start: 0.9440 (mp) cc_final: 0.8906 (tp) REVERT: A 425 ASN cc_start: 0.8063 (p0) cc_final: 0.7599 (p0) REVERT: A 494 LEU cc_start: 0.8845 (mt) cc_final: 0.7996 (mt) REVERT: B 528 SER cc_start: 0.9327 (m) cc_final: 0.8677 (p) REVERT: B 601 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7418 (mtmm) REVERT: B 626 MET cc_start: 0.8431 (mmp) cc_final: 0.7954 (mmm) REVERT: C 104 MET cc_start: 0.8938 (ttm) cc_final: 0.8726 (ttt) REVERT: C 150 MET cc_start: 0.9074 (mmp) cc_final: 0.8814 (mmt) REVERT: C 186 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7316 (ptm160) REVERT: D 584 GLU cc_start: 0.9348 (tt0) cc_final: 0.8853 (tp30) REVERT: D 626 MET cc_start: 0.9483 (mmp) cc_final: 0.9175 (tpp) REVERT: D 650 GLN cc_start: 0.8637 (tp-100) cc_final: 0.7675 (tp-100) REVERT: E 69 TRP cc_start: 0.8869 (m-90) cc_final: 0.8313 (m-90) REVERT: E 100 MET cc_start: 0.9305 (mtm) cc_final: 0.9098 (mtp) REVERT: E 279 ASN cc_start: 0.8831 (t0) cc_final: 0.8203 (t0) REVERT: E 453 ILE cc_start: 0.8664 (mm) cc_final: 0.8341 (tp) REVERT: F 530 MET cc_start: 0.9044 (mtp) cc_final: 0.8607 (mtp) REVERT: F 633 LYS cc_start: 0.9685 (mttt) cc_final: 0.9326 (mmmt) REVERT: F 650 GLN cc_start: 0.7548 (tp40) cc_final: 0.6595 (tp40) REVERT: F 655 LYS cc_start: 0.9624 (ttmm) cc_final: 0.8906 (ttmm) REVERT: H 45 LEU cc_start: 0.9506 (mm) cc_final: 0.9287 (mm) REVERT: H 82 MET cc_start: 0.9456 (ptp) cc_final: 0.9025 (tpt) REVERT: H 100 MET cc_start: 0.9195 (mpp) cc_final: 0.8970 (mpp) REVERT: L 35 TRP cc_start: 0.7909 (m100) cc_final: 0.7691 (m100) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2571 time to fit residues: 72.6321 Evaluate side-chains 124 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 5.9990 chunk 134 optimal weight: 0.0870 chunk 29 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 188 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.039002 restraints weight = 98732.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.040607 restraints weight = 58695.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.041759 restraints weight = 41027.892| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17295 Z= 0.129 Angle : 0.636 9.677 23679 Z= 0.310 Chirality : 0.045 0.249 2913 Planarity : 0.007 0.312 2833 Dihedral : 6.966 58.723 4264 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.19), residues: 1918 helix: 0.72 (0.27), residues: 381 sheet: -0.20 (0.22), residues: 546 loop : -0.58 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 69 HIS 0.006 0.001 HIS A 249 PHE 0.012 0.001 PHE E 383 TYR 0.032 0.002 TYR F 586 ARG 0.027 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 60) link_NAG-ASN : angle 2.07026 ( 180) link_ALPHA1-6 : bond 0.01287 ( 4) link_ALPHA1-6 : angle 1.53235 ( 12) link_BETA1-4 : bond 0.00544 ( 36) link_BETA1-4 : angle 2.13181 ( 108) link_ALPHA1-3 : bond 0.00807 ( 5) link_ALPHA1-3 : angle 2.16135 ( 15) hydrogen bonds : bond 0.03748 ( 480) hydrogen bonds : angle 5.35350 ( 1245) SS BOND : bond 0.00549 ( 34) SS BOND : angle 1.07044 ( 68) covalent geometry : bond 0.00274 (17156) covalent geometry : angle 0.59072 (23296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8377 (ptp) cc_final: 0.8083 (ptt) REVERT: A 201 ILE cc_start: 0.9414 (mp) cc_final: 0.8868 (tp) REVERT: A 425 ASN cc_start: 0.7994 (p0) cc_final: 0.7583 (p0) REVERT: A 434 MET cc_start: 0.8555 (tpp) cc_final: 0.8163 (tpp) REVERT: A 494 LEU cc_start: 0.8824 (mt) cc_final: 0.8070 (mt) REVERT: B 528 SER cc_start: 0.9338 (m) cc_final: 0.8688 (p) REVERT: B 529 THR cc_start: 0.9375 (p) cc_final: 0.9157 (t) REVERT: B 530 MET cc_start: 0.8528 (tpp) cc_final: 0.8144 (tpp) REVERT: B 626 MET cc_start: 0.8408 (mmp) cc_final: 0.7983 (mmm) REVERT: B 647 GLU cc_start: 0.9380 (tt0) cc_final: 0.9080 (tt0) REVERT: B 655 LYS cc_start: 0.9333 (pttp) cc_final: 0.9068 (pptt) REVERT: C 150 MET cc_start: 0.9090 (mmp) cc_final: 0.8811 (mmt) REVERT: C 186 ARG cc_start: 0.8314 (mmp80) cc_final: 0.7392 (ptm160) REVERT: C 475 MET cc_start: 0.8804 (mmp) cc_final: 0.8587 (mmm) REVERT: D 584 GLU cc_start: 0.9313 (tt0) cc_final: 0.8837 (tp30) REVERT: D 610 TRP cc_start: 0.7057 (p90) cc_final: 0.6350 (p90) REVERT: D 626 MET cc_start: 0.9438 (mmp) cc_final: 0.9168 (tpp) REVERT: D 650 GLN cc_start: 0.8684 (tp-100) cc_final: 0.7790 (tp-100) REVERT: E 69 TRP cc_start: 0.8863 (m-90) cc_final: 0.8272 (m-90) REVERT: E 100 MET cc_start: 0.9259 (mtm) cc_final: 0.9005 (mtp) REVERT: E 165 LEU cc_start: 0.9543 (tp) cc_final: 0.9260 (tt) REVERT: E 279 ASN cc_start: 0.8765 (t0) cc_final: 0.8131 (t0) REVERT: E 434 MET cc_start: 0.8468 (mtm) cc_final: 0.8199 (mtt) REVERT: E 453 ILE cc_start: 0.8658 (mm) cc_final: 0.8361 (tp) REVERT: F 530 MET cc_start: 0.8967 (mtp) cc_final: 0.8487 (mtp) REVERT: F 633 LYS cc_start: 0.9680 (mttt) cc_final: 0.9322 (mmmt) REVERT: F 650 GLN cc_start: 0.7275 (tp40) cc_final: 0.6359 (tp40) REVERT: F 655 LYS cc_start: 0.9544 (ttmm) cc_final: 0.8944 (ttmm) REVERT: H 34 MET cc_start: 0.8472 (mmm) cc_final: 0.7849 (mmm) REVERT: H 45 LEU cc_start: 0.9487 (mm) cc_final: 0.9210 (mm) REVERT: H 82 MET cc_start: 0.9436 (ptp) cc_final: 0.9038 (tpt) REVERT: L 35 TRP cc_start: 0.7854 (m100) cc_final: 0.6889 (m100) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2577 time to fit residues: 71.1736 Evaluate side-chains 135 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 607 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3028 r_free = 0.3028 target = 0.049963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.038173 restraints weight = 100410.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.039720 restraints weight = 60610.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.040828 restraints weight = 42719.804| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17295 Z= 0.155 Angle : 0.648 9.415 23679 Z= 0.318 Chirality : 0.045 0.254 2913 Planarity : 0.006 0.245 2833 Dihedral : 6.905 57.956 4264 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.43 (0.19), residues: 1918 helix: 0.64 (0.27), residues: 384 sheet: -0.27 (0.22), residues: 544 loop : -0.59 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 69 HIS 0.007 0.001 HIS A 249 PHE 0.010 0.002 PHE E 382 TYR 0.037 0.002 TYR D 638 ARG 0.023 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 60) link_NAG-ASN : angle 2.02236 ( 180) link_ALPHA1-6 : bond 0.01163 ( 4) link_ALPHA1-6 : angle 1.46193 ( 12) link_BETA1-4 : bond 0.00497 ( 36) link_BETA1-4 : angle 2.13236 ( 108) link_ALPHA1-3 : bond 0.00722 ( 5) link_ALPHA1-3 : angle 2.26564 ( 15) hydrogen bonds : bond 0.03836 ( 480) hydrogen bonds : angle 5.34413 ( 1245) SS BOND : bond 0.00283 ( 34) SS BOND : angle 1.04090 ( 68) covalent geometry : bond 0.00333 (17156) covalent geometry : angle 0.60497 (23296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8569 (ptp) cc_final: 0.8330 (ptt) REVERT: A 201 ILE cc_start: 0.9403 (mp) cc_final: 0.8895 (tp) REVERT: A 425 ASN cc_start: 0.8028 (p0) cc_final: 0.7593 (p0) REVERT: A 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8070 (mt) REVERT: B 528 SER cc_start: 0.9376 (m) cc_final: 0.8881 (p) REVERT: B 601 LYS cc_start: 0.8362 (mmtm) cc_final: 0.7485 (mtmm) REVERT: B 633 LYS cc_start: 0.9572 (mtmm) cc_final: 0.9332 (mtmm) REVERT: B 655 LYS cc_start: 0.9333 (pttp) cc_final: 0.9059 (pptt) REVERT: C 150 MET cc_start: 0.9075 (mmp) cc_final: 0.8723 (mmp) REVERT: C 186 ARG cc_start: 0.8375 (mmp80) cc_final: 0.7458 (ptm160) REVERT: C 475 MET cc_start: 0.8840 (mmp) cc_final: 0.8625 (mmm) REVERT: D 584 GLU cc_start: 0.9323 (tt0) cc_final: 0.8771 (tp30) REVERT: D 610 TRP cc_start: 0.7277 (p90) cc_final: 0.6755 (p90) REVERT: D 626 MET cc_start: 0.9438 (mmp) cc_final: 0.9186 (tpp) REVERT: D 650 GLN cc_start: 0.8715 (tp-100) cc_final: 0.7944 (tp-100) REVERT: E 69 TRP cc_start: 0.8835 (m-90) cc_final: 0.8221 (m-10) REVERT: E 165 LEU cc_start: 0.9482 (tp) cc_final: 0.9188 (tt) REVERT: E 279 ASN cc_start: 0.8854 (t0) cc_final: 0.8270 (t0) REVERT: E 434 MET cc_start: 0.8472 (mtm) cc_final: 0.8065 (mtt) REVERT: E 453 ILE cc_start: 0.8694 (mm) cc_final: 0.8375 (tp) REVERT: F 530 MET cc_start: 0.8917 (mtp) cc_final: 0.8407 (ttm) REVERT: F 633 LYS cc_start: 0.9684 (mttt) cc_final: 0.9319 (mmmt) REVERT: F 650 GLN cc_start: 0.7368 (tp40) cc_final: 0.6616 (tp40) REVERT: F 655 LYS cc_start: 0.9629 (ttmm) cc_final: 0.8973 (ttmm) REVERT: F 660 LEU cc_start: 0.8014 (mm) cc_final: 0.7739 (pp) REVERT: H 34 MET cc_start: 0.8742 (mmm) cc_final: 0.8062 (mmm) REVERT: H 82 MET cc_start: 0.9508 (ptp) cc_final: 0.9045 (tpt) REVERT: L 23 CYS cc_start: 0.4595 (p) cc_final: 0.3651 (p) REVERT: L 35 TRP cc_start: 0.8151 (m100) cc_final: 0.7255 (m100) REVERT: L 89 LYS cc_start: 0.9230 (ttpp) cc_final: 0.9005 (tmmt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2544 time to fit residues: 70.6672 Evaluate side-chains 128 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 91 optimal weight: 10.0000 chunk 21 optimal weight: 0.0770 chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 168 optimal weight: 30.0000 chunk 31 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN E 374 HIS F 570 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.039327 restraints weight = 98518.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.040954 restraints weight = 58251.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.042118 restraints weight = 40596.181| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17295 Z= 0.113 Angle : 0.616 10.011 23679 Z= 0.301 Chirality : 0.045 0.311 2913 Planarity : 0.006 0.233 2833 Dihedral : 6.660 57.351 4264 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1918 helix: 0.77 (0.28), residues: 384 sheet: -0.16 (0.23), residues: 544 loop : -0.53 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 69 HIS 0.006 0.001 HIS E 249 PHE 0.012 0.001 PHE E 383 TYR 0.015 0.001 TYR F 586 ARG 0.022 0.000 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 60) link_NAG-ASN : angle 2.06360 ( 180) link_ALPHA1-6 : bond 0.01235 ( 4) link_ALPHA1-6 : angle 1.26563 ( 12) link_BETA1-4 : bond 0.00569 ( 36) link_BETA1-4 : angle 2.01794 ( 108) link_ALPHA1-3 : bond 0.00793 ( 5) link_ALPHA1-3 : angle 2.25787 ( 15) hydrogen bonds : bond 0.03605 ( 480) hydrogen bonds : angle 5.21006 ( 1245) SS BOND : bond 0.00286 ( 34) SS BOND : angle 0.88661 ( 68) covalent geometry : bond 0.00243 (17156) covalent geometry : angle 0.57197 (23296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8569 (ptp) cc_final: 0.8326 (ptt) REVERT: A 201 ILE cc_start: 0.9376 (mp) cc_final: 0.8879 (tp) REVERT: A 425 ASN cc_start: 0.7919 (p0) cc_final: 0.7523 (p0) REVERT: A 494 LEU cc_start: 0.8750 (mt) cc_final: 0.8095 (mt) REVERT: B 528 SER cc_start: 0.9396 (m) cc_final: 0.9077 (t) REVERT: B 530 MET cc_start: 0.8482 (tpp) cc_final: 0.7841 (tpp) REVERT: B 601 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7972 (mmmm) REVERT: B 626 MET cc_start: 0.8430 (mmm) cc_final: 0.7779 (mmm) REVERT: B 647 GLU cc_start: 0.9450 (tt0) cc_final: 0.8879 (tp30) REVERT: B 651 ASN cc_start: 0.9431 (p0) cc_final: 0.8690 (p0) REVERT: B 655 LYS cc_start: 0.9327 (pttp) cc_final: 0.9081 (pptt) REVERT: C 150 MET cc_start: 0.9122 (mmp) cc_final: 0.8829 (mmt) REVERT: D 584 GLU cc_start: 0.9313 (tt0) cc_final: 0.8756 (tp30) REVERT: D 610 TRP cc_start: 0.7370 (p90) cc_final: 0.6741 (p90) REVERT: D 626 MET cc_start: 0.9434 (mmp) cc_final: 0.9174 (tpp) REVERT: D 650 GLN cc_start: 0.8647 (tp-100) cc_final: 0.7926 (tp-100) REVERT: E 69 TRP cc_start: 0.8852 (m-90) cc_final: 0.8259 (m-10) REVERT: E 103 GLN cc_start: 0.9213 (tp40) cc_final: 0.8682 (tp-100) REVERT: E 165 LEU cc_start: 0.9484 (tp) cc_final: 0.9204 (tt) REVERT: E 279 ASN cc_start: 0.8787 (t0) cc_final: 0.8255 (t0) REVERT: E 434 MET cc_start: 0.8328 (mtm) cc_final: 0.8115 (mtt) REVERT: E 453 ILE cc_start: 0.8652 (mm) cc_final: 0.8360 (tp) REVERT: E 478 ASN cc_start: 0.9055 (t0) cc_final: 0.8566 (t0) REVERT: E 479 TRP cc_start: 0.9218 (m-90) cc_final: 0.8491 (m-90) REVERT: F 530 MET cc_start: 0.8880 (mtp) cc_final: 0.8445 (mtp) REVERT: F 633 LYS cc_start: 0.9674 (mttt) cc_final: 0.9314 (mmmt) REVERT: F 650 GLN cc_start: 0.7541 (tp40) cc_final: 0.6365 (tp40) REVERT: F 655 LYS cc_start: 0.9542 (ttmm) cc_final: 0.8900 (ttmm) REVERT: F 660 LEU cc_start: 0.7949 (mm) cc_final: 0.7677 (pp) REVERT: H 34 MET cc_start: 0.8839 (mmm) cc_final: 0.8251 (mmm) REVERT: H 45 LEU cc_start: 0.9507 (mm) cc_final: 0.9215 (mm) REVERT: H 82 MET cc_start: 0.9474 (ptp) cc_final: 0.8988 (tpt) REVERT: L 23 CYS cc_start: 0.4495 (p) cc_final: 0.3514 (p) REVERT: L 35 TRP cc_start: 0.8085 (m100) cc_final: 0.7218 (m100) REVERT: L 89 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8755 (tmmt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2576 time to fit residues: 72.0744 Evaluate side-chains 134 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 651 ASN F 570 HIS ** H 35 HIS ** 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 = 0.3012 r_free = 0.3012 target = 0.049369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.037732 restraints weight = 101213.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.039251 restraints weight = 60890.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.040342 restraints weight = 42949.050| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17295 Z= 0.190 Angle : 0.686 9.766 23679 Z= 0.336 Chirality : 0.045 0.298 2913 Planarity : 0.006 0.220 2833 Dihedral : 6.879 57.850 4264 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.46 (0.19), residues: 1918 helix: 0.60 (0.27), residues: 381 sheet: -0.29 (0.22), residues: 550 loop : -0.60 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP A 69 HIS 0.006 0.002 HIS A 105 PHE 0.011 0.002 PHE E 382 TYR 0.022 0.002 TYR F 586 ARG 0.018 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 60) link_NAG-ASN : angle 2.12116 ( 180) link_ALPHA1-6 : bond 0.01376 ( 4) link_ALPHA1-6 : angle 1.51365 ( 12) link_BETA1-4 : bond 0.00474 ( 36) link_BETA1-4 : angle 2.15450 ( 108) link_ALPHA1-3 : bond 0.00459 ( 5) link_ALPHA1-3 : angle 2.37137 ( 15) hydrogen bonds : bond 0.03977 ( 480) hydrogen bonds : angle 5.41295 ( 1245) SS BOND : bond 0.00333 ( 34) SS BOND : angle 1.00517 ( 68) covalent geometry : bond 0.00405 (17156) covalent geometry : angle 0.64384 (23296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.52 seconds wall clock time: 78 minutes 4.99 seconds (4684.99 seconds total)