Starting phenix.real_space_refine on Sun Jun 15 03:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.map" model { file = "/net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t76_25735/06_2025/7t76_25735.cif" } resolution = 4.43 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= 0.003 sd= 0.093 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 106 5.16 5 C 10329 2.51 5 N 2742 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 16587 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 791 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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 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 Time building chain proxies: 10.60, per 1000 atoms: 0.64 Number of scatterers: 16587 At special positions: 0 Unit cell: (129.95, 132.25, 161, 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 106 16.00 O 3410 8.00 N 2742 7.00 C 10329 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=2.21 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.09 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 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=2.04 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=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.01 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=2.13 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " 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 Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG 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 276 " " NAG A 605 " - " 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 276 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 88 " " 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 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 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 1.9 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 27 sheets defined 24.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 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 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.653A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.773A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.783A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (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 541 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 573 through 596 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 659 removed outlier: 3.802A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) 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 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.870A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.778A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 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 661 removed outlier: 4.375A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 650 through 658 Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'L' and resid 79 through 83 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 sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 5.698A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.862A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.484A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, 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 312 removed outlier: 6.682A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 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=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.432A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 removed outlier: 7.527A pdb=" N HIS C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 215 through 218 removed outlier: 5.379A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AB5, 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 298 removed outlier: 7.022A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 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=AB6, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.782A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 496 removed outlier: 5.485A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.609A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.856A pdb=" N ARG E 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 100B" --> pdb=" O TYS H 100E" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AC5, 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 312 removed outlier: 6.821A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 removed outlier: 4.353A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 466 through 470 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 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 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 18 through 24 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 460 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4817 1.34 - 1.49: 5235 1.49 - 1.64: 6711 1.64 - 1.79: 54 1.79 - 1.94: 88 Bond restraints: 16905 Sorted by residual: bond pdb=" NE1 TRP B 610 " pdb=" CE2 TRP B 610 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.33e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sigma weight residual 1.522 1.564 -0.041 7.00e-03 2.04e+04 3.47e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.644 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 22907 7.78 - 15.55: 44 15.55 - 23.33: 0 23.33 - 31.11: 0 31.11 - 38.88: 11 Bond angle restraints: 22962 Sorted by residual: angle pdb=" C2 NAG E 604 " pdb=" N2 NAG E 604 " pdb=" C7 NAG E 604 " ideal model delta sigma weight residual 124.56 163.44 -38.88 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.08 -38.52 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C2 NAG D 703 " pdb=" N2 NAG D 703 " pdb=" C7 NAG D 703 " ideal model delta sigma weight residual 124.56 162.44 -37.88 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 161.76 -37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 161.29 -36.73 3.00e+00 1.11e-01 1.50e+02 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 11033 21.84 - 43.67: 281 43.67 - 65.50: 77 65.50 - 87.34: 54 87.34 - 109.17: 25 Dihedral angle restraints: 11470 sinusoidal: 5892 harmonic: 5578 Sorted by residual: 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 -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 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 -86.00 -169.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 11467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2110 0.132 - 0.263: 499 0.263 - 0.395: 203 0.395 - 0.527: 66 0.527 - 0.659: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.99e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+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 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 ... (remaining 2876 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.373 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" C7 NAG Z 1 " 0.092 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.557 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG S 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG S 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.109 2.00e-02 2.50e+03 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 13 1.40 - 2.28: 43 2.28 - 3.15: 13738 3.15 - 4.03: 43120 4.03 - 4.90: 75419 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132333 Sorted by model distance: nonbonded pdb=" C ASN E 234 " pdb=" C2 NAG E 607 " model vdw 0.530 2.960 nonbonded pdb=" CA ASN E 234 " pdb=" C3 NAG E 607 " model vdw 0.700 3.900 nonbonded pdb=" O ASN E 234 " pdb=" N2 NAG E 607 " model vdw 0.816 3.120 nonbonded pdb=" CB PHE E 233 " pdb=" O6 NAG E 607 " model vdw 0.928 3.440 nonbonded pdb=" CA ASN E 234 " pdb=" O3 NAG E 607 " model vdw 0.962 3.470 ... (remaining 132328 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 605)) selection = (chain 'E' and (resid 32 through 502 or resid 601 through 605)) } 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 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'i' } ncs_group { reference = (chain 'Z' and (resid 1 or resid 4 through 6)) selection = (chain 'j' and (resid 2 or resid 5 through 7)) } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.530 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.024 0.985 17044 Z= 1.536 Angle : 2.010 38.881 23339 Z= 1.180 Chirality : 0.143 0.659 2879 Planarity : 0.017 0.318 2788 Dihedral : 12.894 109.174 7774 Min Nonbonded Distance : 0.530 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.38 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 1.00 % Favored : 98.23 % Cbeta Deviations : 0.11 % 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: 0.31 (0.19), residues: 1894 helix: -0.17 (0.24), residues: 378 sheet: 0.62 (0.22), residues: 508 loop : 0.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP E 96 HIS 0.017 0.003 HIS C 249 PHE 0.032 0.006 PHE E 233 TYR 0.058 0.008 TYR C 40 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.07423 ( 55) link_NAG-ASN : angle 3.16228 ( 165) link_ALPHA1-6 : bond 0.00309 ( 7) link_ALPHA1-6 : angle 1.42300 ( 21) link_BETA1-4 : bond 0.06022 ( 34) link_BETA1-4 : angle 5.02996 ( 102) link_ALPHA1-3 : bond 0.00409 ( 7) link_ALPHA1-3 : angle 2.62497 ( 21) hydrogen bonds : bond 0.17061 ( 460) hydrogen bonds : angle 7.63151 ( 1200) SS BOND : bond 0.05257 ( 34) SS BOND : angle 3.45474 ( 68) covalent geometry : bond 0.02162 (16905) covalent geometry : angle 1.96917 (22962) Misc. bond : bond 0.90660 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 436 time to evaluate : 1.911 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ILE cc_start: 0.9408 (pt) cc_final: 0.9198 (mp) REVERT: A 254 VAL cc_start: 0.9515 (t) cc_final: 0.9125 (p) REVERT: A 374 HIS cc_start: 0.7329 (t-170) cc_final: 0.6929 (t-90) REVERT: C 69 TRP cc_start: 0.8404 (m-90) cc_final: 0.7707 (m-10) REVERT: C 122 LEU cc_start: 0.9362 (mt) cc_final: 0.9132 (mp) REVERT: C 136 ASN cc_start: 0.6442 (t0) cc_final: 0.6058 (m110) REVERT: D 593 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (mm) REVERT: D 610 TRP cc_start: 0.6222 (p90) cc_final: 0.5985 (p-90) REVERT: D 655 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8525 (mmmm) REVERT: E 42 VAL cc_start: 0.9298 (t) cc_final: 0.9025 (p) REVERT: E 165 LEU cc_start: 0.9258 (mt) cc_final: 0.8939 (mp) REVERT: E 180 ASP cc_start: 0.8583 (m-30) cc_final: 0.8381 (m-30) REVERT: E 186 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: E 373 THR cc_start: 0.9127 (p) cc_final: 0.8925 (p) REVERT: E 450 THR cc_start: 0.9263 (p) cc_final: 0.9044 (p) REVERT: F 538 THR cc_start: 0.8610 (p) cc_final: 0.8342 (p) REVERT: F 581 LEU cc_start: 0.9404 (tp) cc_final: 0.9204 (tt) REVERT: F 606 THR cc_start: 0.8958 (p) cc_final: 0.8590 (t) REVERT: F 607 ASN cc_start: 0.8474 (m-40) cc_final: 0.8109 (p0) REVERT: F 624 ASP cc_start: 0.8399 (m-30) cc_final: 0.7952 (t0) REVERT: F 652 GLN cc_start: 0.7896 (tp40) cc_final: 0.7634 (tp40) REVERT: B 543 ASN cc_start: 0.8074 (m-40) cc_final: 0.7841 (t0) REVERT: B 584 GLU cc_start: 0.8922 (tt0) cc_final: 0.8246 (tp30) REVERT: B 643 TYR cc_start: 0.8935 (m-10) cc_final: 0.8038 (m-10) REVERT: L 34 SER cc_start: 0.8990 (m) cc_final: 0.8773 (p) REVERT: L 39 HIS cc_start: 0.8878 (t-90) cc_final: 0.8579 (m-70) REVERT: L 50 GLU cc_start: 0.8511 (tt0) cc_final: 0.8065 (tm-30) REVERT: L 53 ASN cc_start: 0.8897 (m-40) cc_final: 0.8135 (m-40) REVERT: L 91 TYR cc_start: 0.7852 (t80) cc_final: 0.7552 (t80) REVERT: L 98 PHE cc_start: 0.8669 (m-80) cc_final: 0.8435 (m-80) REVERT: H 18 LEU cc_start: 0.8334 (tt) cc_final: 0.7591 (tt) REVERT: H 20 LEU cc_start: 0.9316 (mt) cc_final: 0.8906 (mt) REVERT: H 29 PHE cc_start: 0.8789 (t80) cc_final: 0.8174 (t80) REVERT: H 43 LYS cc_start: 0.8998 (mptt) cc_final: 0.8450 (pttp) REVERT: H 53 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7671 (p0) REVERT: H 68 THR cc_start: 0.9158 (m) cc_final: 0.8738 (t) outliers start: 13 outliers final: 2 residues processed: 448 average time/residue: 0.2948 time to fit residues: 194.0830 Evaluate side-chains 227 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 167 ASN C 190 HIS C 363 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 374 HIS F 591 GLN ** L 17 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 = 0.3318 r_free = 0.3318 target = 0.068950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.052706 restraints weight = 68414.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054711 restraints weight = 39529.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056124 restraints weight = 27337.537| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17044 Z= 0.190 Angle : 0.905 20.681 23339 Z= 0.423 Chirality : 0.053 0.717 2879 Planarity : 0.004 0.045 2788 Dihedral : 11.549 80.855 4217 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1894 helix: 0.21 (0.26), residues: 417 sheet: 0.42 (0.22), residues: 522 loop : -0.19 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 96 HIS 0.006 0.001 HIS E 249 PHE 0.038 0.002 PHE E 233 TYR 0.017 0.002 TYR E 435 ARG 0.012 0.001 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 55) link_NAG-ASN : angle 4.04922 ( 165) link_ALPHA1-6 : bond 0.00517 ( 7) link_ALPHA1-6 : angle 1.79138 ( 21) link_BETA1-4 : bond 0.00844 ( 34) link_BETA1-4 : angle 3.37677 ( 102) link_ALPHA1-3 : bond 0.00669 ( 7) link_ALPHA1-3 : angle 2.56785 ( 21) hydrogen bonds : bond 0.05971 ( 460) hydrogen bonds : angle 6.02180 ( 1200) SS BOND : bond 0.00454 ( 34) SS BOND : angle 1.33122 ( 68) covalent geometry : bond 0.00416 (16905) covalent geometry : angle 0.80572 (22962) Misc. bond : bond 0.00387 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.918 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: A 98 ASN cc_start: 0.8597 (t0) cc_final: 0.7560 (m-40) REVERT: A 181 ILE cc_start: 0.9468 (pt) cc_final: 0.8991 (mm) REVERT: A 374 HIS cc_start: 0.7797 (t-170) cc_final: 0.7497 (t-90) REVERT: C 53 PHE cc_start: 0.8260 (m-80) cc_final: 0.7908 (m-80) REVERT: C 69 TRP cc_start: 0.8596 (m-90) cc_final: 0.8106 (m-10) REVERT: C 95 MET cc_start: 0.7922 (mmp) cc_final: 0.7651 (mmp) REVERT: C 111 LEU cc_start: 0.9487 (mm) cc_final: 0.9082 (mt) REVERT: C 122 LEU cc_start: 0.9528 (mt) cc_final: 0.9318 (mm) REVERT: C 136 ASN cc_start: 0.6392 (t0) cc_final: 0.6153 (m110) REVERT: C 210 PHE cc_start: 0.8651 (m-80) cc_final: 0.8117 (m-10) REVERT: C 260 LEU cc_start: 0.9303 (mt) cc_final: 0.9030 (mt) REVERT: D 584 GLU cc_start: 0.9061 (tp30) cc_final: 0.8209 (tm-30) REVERT: D 607 ASN cc_start: 0.8448 (m110) cc_final: 0.8094 (p0) REVERT: D 657 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8597 (mp0) REVERT: E 180 ASP cc_start: 0.8753 (m-30) cc_final: 0.8394 (m-30) REVERT: E 315 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8875 (mp10) REVERT: E 426 MET cc_start: 0.7327 (ttp) cc_final: 0.7126 (ttp) REVERT: F 574 LYS cc_start: 0.6633 (pttm) cc_final: 0.6059 (mmpt) REVERT: F 607 ASN cc_start: 0.8440 (m-40) cc_final: 0.7999 (p0) REVERT: F 647 GLU cc_start: 0.8410 (pt0) cc_final: 0.7850 (pt0) REVERT: B 530 MET cc_start: 0.8237 (mtp) cc_final: 0.8000 (ppp) REVERT: B 538 THR cc_start: 0.9122 (t) cc_final: 0.8895 (t) REVERT: B 584 GLU cc_start: 0.8709 (tt0) cc_final: 0.8228 (tp30) REVERT: B 632 ASP cc_start: 0.9170 (t0) cc_final: 0.8859 (p0) REVERT: B 643 TYR cc_start: 0.8711 (m-10) cc_final: 0.7990 (m-10) REVERT: L 73 LEU cc_start: 0.9305 (tp) cc_final: 0.9039 (tp) REVERT: L 91 TYR cc_start: 0.8062 (t80) cc_final: 0.7638 (t80) REVERT: L 104 LEU cc_start: 0.7761 (tt) cc_final: 0.6661 (tp) REVERT: H 68 THR cc_start: 0.8768 (m) cc_final: 0.8483 (t) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2787 time to fit residues: 127.4667 Evaluate side-chains 190 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 177 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 190 HIS D 591 GLN D 630 GLN E 85 HIS E 352 HIS F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051888 restraints weight = 68748.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053829 restraints weight = 40213.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055207 restraints weight = 28106.214| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17044 Z= 0.151 Angle : 0.766 19.776 23339 Z= 0.358 Chirality : 0.049 0.481 2879 Planarity : 0.005 0.174 2788 Dihedral : 9.862 70.770 4217 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.04 (0.19), residues: 1894 helix: 0.38 (0.27), residues: 390 sheet: 0.26 (0.21), residues: 553 loop : -0.26 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 96 HIS 0.007 0.001 HIS A 249 PHE 0.043 0.002 PHE E 233 TYR 0.018 0.001 TYR E 484 ARG 0.005 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 55) link_NAG-ASN : angle 3.39522 ( 165) link_ALPHA1-6 : bond 0.00511 ( 7) link_ALPHA1-6 : angle 1.76297 ( 21) link_BETA1-4 : bond 0.00749 ( 34) link_BETA1-4 : angle 2.80826 ( 102) link_ALPHA1-3 : bond 0.00838 ( 7) link_ALPHA1-3 : angle 2.29067 ( 21) hydrogen bonds : bond 0.04653 ( 460) hydrogen bonds : angle 5.54307 ( 1200) SS BOND : bond 0.00354 ( 34) SS BOND : angle 1.00964 ( 68) covalent geometry : bond 0.00330 (16905) covalent geometry : angle 0.68401 (22962) Misc. bond : bond 0.00718 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.725 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 104 MET cc_start: 0.9267 (ttt) cc_final: 0.9038 (ttm) REVERT: A 180 ASP cc_start: 0.8585 (m-30) cc_final: 0.7980 (p0) REVERT: A 286 VAL cc_start: 0.9427 (t) cc_final: 0.9013 (p) REVERT: A 374 HIS cc_start: 0.7783 (t-170) cc_final: 0.7457 (t-90) REVERT: A 494 LEU cc_start: 0.8885 (tt) cc_final: 0.8557 (tt) REVERT: C 53 PHE cc_start: 0.8523 (m-80) cc_final: 0.8242 (m-80) REVERT: C 69 TRP cc_start: 0.8650 (m-90) cc_final: 0.8028 (m-10) REVERT: C 111 LEU cc_start: 0.9449 (mm) cc_final: 0.9012 (mt) REVERT: C 116 LEU cc_start: 0.9322 (tt) cc_final: 0.8868 (mp) REVERT: C 136 ASN cc_start: 0.6708 (t0) cc_final: 0.6463 (m110) REVERT: C 210 PHE cc_start: 0.8720 (m-80) cc_final: 0.8223 (m-10) REVERT: C 426 MET cc_start: 0.9167 (ttp) cc_final: 0.8894 (ttm) REVERT: D 584 GLU cc_start: 0.9153 (tp30) cc_final: 0.8173 (tm-30) REVERT: D 607 ASN cc_start: 0.8397 (m110) cc_final: 0.8015 (p0) REVERT: D 648 GLU cc_start: 0.8767 (pp20) cc_final: 0.8105 (pp20) REVERT: D 657 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8590 (mp0) REVERT: E 180 ASP cc_start: 0.8819 (m-30) cc_final: 0.8301 (m-30) REVERT: E 315 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8783 (mp10) REVERT: F 574 LYS cc_start: 0.7894 (pttm) cc_final: 0.7433 (mmpt) REVERT: F 576 LEU cc_start: 0.8633 (mt) cc_final: 0.8025 (tt) REVERT: F 606 THR cc_start: 0.8854 (p) cc_final: 0.8439 (t) REVERT: F 607 ASN cc_start: 0.8557 (m-40) cc_final: 0.7989 (p0) REVERT: F 647 GLU cc_start: 0.8524 (pt0) cc_final: 0.8146 (pt0) REVERT: B 536 THR cc_start: 0.9309 (p) cc_final: 0.8964 (p) REVERT: B 540 GLN cc_start: 0.9251 (mm110) cc_final: 0.8100 (mt0) REVERT: B 584 GLU cc_start: 0.8749 (tt0) cc_final: 0.8271 (tp30) REVERT: B 601 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8696 (mmmm) REVERT: B 643 TYR cc_start: 0.8706 (m-10) cc_final: 0.7685 (m-10) REVERT: L 49 TYR cc_start: 0.8963 (p90) cc_final: 0.8221 (p90) REVERT: L 53 ASN cc_start: 0.8681 (m-40) cc_final: 0.7953 (t0) REVERT: L 73 LEU cc_start: 0.9312 (tp) cc_final: 0.9018 (tp) REVERT: L 91 TYR cc_start: 0.7957 (t80) cc_final: 0.7567 (t80) REVERT: H 68 THR cc_start: 0.8791 (m) cc_final: 0.8145 (t) REVERT: H 80 LEU cc_start: 0.9166 (tp) cc_final: 0.8837 (tp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2668 time to fit residues: 105.9200 Evaluate side-chains 186 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN D 607 ASN D 630 GLN F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049322 restraints weight = 70818.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051103 restraints weight = 42118.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052391 restraints weight = 29923.306| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17044 Z= 0.206 Angle : 0.773 18.792 23339 Z= 0.363 Chirality : 0.049 0.442 2879 Planarity : 0.004 0.072 2788 Dihedral : 9.060 66.697 4217 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1894 helix: 0.14 (0.26), residues: 405 sheet: -0.00 (0.21), residues: 581 loop : -0.43 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 36 HIS 0.007 0.001 HIS C 190 PHE 0.036 0.002 PHE E 233 TYR 0.016 0.002 TYR E 384 ARG 0.006 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 55) link_NAG-ASN : angle 3.32003 ( 165) link_ALPHA1-6 : bond 0.00468 ( 7) link_ALPHA1-6 : angle 1.78375 ( 21) link_BETA1-4 : bond 0.00628 ( 34) link_BETA1-4 : angle 2.64287 ( 102) link_ALPHA1-3 : bond 0.00763 ( 7) link_ALPHA1-3 : angle 2.52958 ( 21) hydrogen bonds : bond 0.04366 ( 460) hydrogen bonds : angle 5.33619 ( 1200) SS BOND : bond 0.00388 ( 34) SS BOND : angle 1.08072 ( 68) covalent geometry : bond 0.00450 (16905) covalent geometry : angle 0.69657 (22962) Misc. bond : bond 0.00366 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 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: A 104 MET cc_start: 0.9563 (ttt) cc_final: 0.9233 (ttt) REVERT: A 180 ASP cc_start: 0.8686 (m-30) cc_final: 0.8381 (m-30) REVERT: A 374 HIS cc_start: 0.7984 (t-170) cc_final: 0.7667 (t-90) REVERT: A 434 MET cc_start: 0.9041 (ptp) cc_final: 0.8787 (ptt) REVERT: C 53 PHE cc_start: 0.8544 (m-80) cc_final: 0.8088 (m-80) REVERT: C 69 TRP cc_start: 0.8769 (m-90) cc_final: 0.8095 (m-10) REVERT: C 104 MET cc_start: 0.9366 (tmm) cc_final: 0.9023 (tmm) REVERT: C 111 LEU cc_start: 0.9468 (mm) cc_final: 0.9030 (mt) REVERT: C 116 LEU cc_start: 0.9390 (tt) cc_final: 0.9021 (mt) REVERT: C 260 LEU cc_start: 0.9391 (mt) cc_final: 0.9097 (mt) REVERT: D 584 GLU cc_start: 0.9218 (tp30) cc_final: 0.8281 (tm-30) REVERT: D 648 GLU cc_start: 0.8913 (pp20) cc_final: 0.8649 (pp20) REVERT: D 657 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 180 ASP cc_start: 0.8857 (m-30) cc_final: 0.8309 (m-30) REVERT: F 576 LEU cc_start: 0.8737 (mt) cc_final: 0.8133 (tt) REVERT: F 584 GLU cc_start: 0.8593 (tp30) cc_final: 0.7993 (tm-30) REVERT: F 606 THR cc_start: 0.8738 (p) cc_final: 0.8381 (t) REVERT: F 607 ASN cc_start: 0.8458 (m-40) cc_final: 0.7791 (p0) REVERT: F 647 GLU cc_start: 0.8599 (pt0) cc_final: 0.8138 (pt0) REVERT: F 652 GLN cc_start: 0.8242 (tp40) cc_final: 0.8031 (tp-100) REVERT: B 540 GLN cc_start: 0.9275 (mm110) cc_final: 0.8162 (mt0) REVERT: B 584 GLU cc_start: 0.9012 (tt0) cc_final: 0.8282 (tp30) REVERT: B 591 GLN cc_start: 0.9350 (tp40) cc_final: 0.8857 (tp40) REVERT: B 601 LYS cc_start: 0.9069 (mmtm) cc_final: 0.8833 (mmmm) REVERT: B 643 TYR cc_start: 0.8852 (m-10) cc_final: 0.8592 (m-10) REVERT: L 49 TYR cc_start: 0.8983 (p90) cc_final: 0.8081 (p90) REVERT: L 53 ASN cc_start: 0.8757 (m-40) cc_final: 0.8099 (t0) REVERT: L 91 TYR cc_start: 0.7756 (t80) cc_final: 0.7366 (t80) REVERT: H 16 ARG cc_start: 0.9298 (mpt180) cc_final: 0.9058 (mtp180) REVERT: H 68 THR cc_start: 0.8925 (m) cc_final: 0.8607 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2655 time to fit residues: 89.9437 Evaluate side-chains 162 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050565 restraints weight = 70291.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.052448 restraints weight = 40995.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053794 restraints weight = 28629.158| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17044 Z= 0.129 Angle : 0.703 19.267 23339 Z= 0.323 Chirality : 0.048 0.436 2879 Planarity : 0.004 0.044 2788 Dihedral : 8.414 65.930 4217 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1894 helix: 0.15 (0.26), residues: 420 sheet: 0.07 (0.21), residues: 566 loop : -0.46 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.006 0.001 HIS A 249 PHE 0.021 0.001 PHE E 233 TYR 0.010 0.001 TYR A 191 ARG 0.009 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 55) link_NAG-ASN : angle 3.27636 ( 165) link_ALPHA1-6 : bond 0.00541 ( 7) link_ALPHA1-6 : angle 1.75225 ( 21) link_BETA1-4 : bond 0.00678 ( 34) link_BETA1-4 : angle 2.43594 ( 102) link_ALPHA1-3 : bond 0.00896 ( 7) link_ALPHA1-3 : angle 2.30657 ( 21) hydrogen bonds : bond 0.03941 ( 460) hydrogen bonds : angle 5.09353 ( 1200) SS BOND : bond 0.00336 ( 34) SS BOND : angle 0.91687 ( 68) covalent geometry : bond 0.00279 (16905) covalent geometry : angle 0.62293 (22962) Misc. bond : bond 0.00398 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8752 (m-10) cc_final: 0.8377 (m-10) REVERT: A 180 ASP cc_start: 0.8850 (m-30) cc_final: 0.8190 (m-30) REVERT: A 374 HIS cc_start: 0.7941 (t-170) cc_final: 0.7656 (t-90) REVERT: A 434 MET cc_start: 0.8861 (ptp) cc_final: 0.8609 (ptp) REVERT: A 494 LEU cc_start: 0.8810 (tt) cc_final: 0.8496 (tt) REVERT: C 53 PHE cc_start: 0.8523 (m-80) cc_final: 0.8066 (m-80) REVERT: C 69 TRP cc_start: 0.8805 (m-90) cc_final: 0.8081 (m-10) REVERT: C 111 LEU cc_start: 0.9420 (mm) cc_final: 0.9036 (mt) REVERT: C 116 LEU cc_start: 0.9374 (tt) cc_final: 0.9040 (mt) REVERT: C 210 PHE cc_start: 0.8848 (m-80) cc_final: 0.8464 (m-10) REVERT: C 260 LEU cc_start: 0.9267 (mt) cc_final: 0.8922 (mt) REVERT: D 523 LEU cc_start: 0.9129 (mt) cc_final: 0.8928 (mt) REVERT: D 530 MET cc_start: 0.7985 (mtt) cc_final: 0.7742 (mtt) REVERT: D 584 GLU cc_start: 0.9222 (tp30) cc_final: 0.8320 (tm-30) REVERT: D 648 GLU cc_start: 0.8900 (pp20) cc_final: 0.8671 (tm-30) REVERT: E 180 ASP cc_start: 0.8915 (m-30) cc_final: 0.8319 (m-30) REVERT: F 530 MET cc_start: 0.8069 (mmp) cc_final: 0.7301 (mmt) REVERT: F 576 LEU cc_start: 0.8618 (mt) cc_final: 0.8016 (tt) REVERT: F 584 GLU cc_start: 0.8538 (tp30) cc_final: 0.7871 (tm-30) REVERT: F 647 GLU cc_start: 0.8445 (pt0) cc_final: 0.8045 (pt0) REVERT: F 652 GLN cc_start: 0.8268 (tp40) cc_final: 0.7792 (tp-100) REVERT: B 540 GLN cc_start: 0.9232 (mm110) cc_final: 0.8091 (mt0) REVERT: B 584 GLU cc_start: 0.8857 (tt0) cc_final: 0.8122 (tp30) REVERT: B 591 GLN cc_start: 0.9233 (tp40) cc_final: 0.8859 (tp40) REVERT: B 601 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8734 (mmmm) REVERT: B 602 LEU cc_start: 0.9355 (mm) cc_final: 0.9124 (mm) REVERT: B 643 TYR cc_start: 0.8888 (m-10) cc_final: 0.8376 (m-10) REVERT: L 49 TYR cc_start: 0.8945 (p90) cc_final: 0.8225 (p90) REVERT: L 53 ASN cc_start: 0.8787 (m-40) cc_final: 0.8084 (t0) REVERT: L 91 TYR cc_start: 0.7713 (t80) cc_final: 0.7392 (t80) REVERT: H 13 GLN cc_start: 0.8805 (mm110) cc_final: 0.8436 (mm-40) REVERT: H 68 THR cc_start: 0.8791 (m) cc_final: 0.8370 (p) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2564 time to fit residues: 91.4252 Evaluate side-chains 166 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN E 85 HIS E 478 ASN F 585 HIS B 575 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS ** H 35 HIS ** 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 = 0.3220 r_free = 0.3220 target = 0.064464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047789 restraints weight = 72776.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.049585 restraints weight = 43091.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050837 restraints weight = 30473.053| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 17044 Z= 0.241 Angle : 0.787 18.544 23339 Z= 0.371 Chirality : 0.049 0.440 2879 Planarity : 0.004 0.050 2788 Dihedral : 8.252 67.285 4217 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -0.42 (0.19), residues: 1894 helix: 0.40 (0.27), residues: 390 sheet: -0.17 (0.21), residues: 569 loop : -0.54 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.007 0.001 HIS F 585 PHE 0.017 0.002 PHE E 233 TYR 0.013 0.002 TYR E 384 ARG 0.008 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 55) link_NAG-ASN : angle 3.20458 ( 165) link_ALPHA1-6 : bond 0.00557 ( 7) link_ALPHA1-6 : angle 1.88003 ( 21) link_BETA1-4 : bond 0.00584 ( 34) link_BETA1-4 : angle 2.47677 ( 102) link_ALPHA1-3 : bond 0.00778 ( 7) link_ALPHA1-3 : angle 2.53572 ( 21) hydrogen bonds : bond 0.04250 ( 460) hydrogen bonds : angle 5.39517 ( 1200) SS BOND : bond 0.00443 ( 34) SS BOND : angle 1.12767 ( 68) covalent geometry : bond 0.00533 (16905) covalent geometry : angle 0.71774 (22962) Misc. bond : bond 0.00289 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.977 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 104 MET cc_start: 0.9505 (ttt) cc_final: 0.9257 (ttm) REVERT: A 180 ASP cc_start: 0.8829 (m-30) cc_final: 0.8584 (m-30) REVERT: A 374 HIS cc_start: 0.7842 (t-170) cc_final: 0.7589 (t-90) REVERT: A 434 MET cc_start: 0.9224 (ptp) cc_final: 0.8850 (ptp) REVERT: C 53 PHE cc_start: 0.8617 (m-80) cc_final: 0.7993 (m-80) REVERT: C 69 TRP cc_start: 0.8870 (m-90) cc_final: 0.7725 (m-10) REVERT: C 104 MET cc_start: 0.9226 (tmm) cc_final: 0.8975 (tmm) REVERT: C 111 LEU cc_start: 0.9475 (mm) cc_final: 0.9065 (mt) REVERT: C 207 LYS cc_start: 0.8458 (pttt) cc_final: 0.8227 (tptt) REVERT: C 260 LEU cc_start: 0.9312 (mt) cc_final: 0.9019 (mt) REVERT: D 584 GLU cc_start: 0.9207 (tp30) cc_final: 0.8367 (tm-30) REVERT: D 655 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8774 (ptpp) REVERT: D 657 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8278 (mt-10) REVERT: E 180 ASP cc_start: 0.8926 (m-30) cc_final: 0.8350 (m-30) REVERT: F 530 MET cc_start: 0.7969 (mmp) cc_final: 0.7124 (mmp) REVERT: F 576 LEU cc_start: 0.8688 (mt) cc_final: 0.8075 (tt) REVERT: F 584 GLU cc_start: 0.8597 (tp30) cc_final: 0.8088 (tm-30) REVERT: F 591 GLN cc_start: 0.9456 (tt0) cc_final: 0.8873 (tt0) REVERT: F 647 GLU cc_start: 0.8499 (pt0) cc_final: 0.8057 (pt0) REVERT: B 540 GLN cc_start: 0.9243 (mm110) cc_final: 0.8170 (mt0) REVERT: B 601 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8836 (mmmm) REVERT: B 607 ASN cc_start: 0.8321 (m-40) cc_final: 0.8090 (m-40) REVERT: L 50 GLU cc_start: 0.8475 (tt0) cc_final: 0.8220 (tt0) REVERT: L 91 TYR cc_start: 0.7690 (t80) cc_final: 0.7350 (t80) REVERT: H 13 GLN cc_start: 0.8848 (mm110) cc_final: 0.8442 (mm-40) REVERT: H 68 THR cc_start: 0.8620 (m) cc_final: 0.8064 (p) REVERT: H 83 ARG cc_start: 0.8374 (mpp80) cc_final: 0.7979 (mpp80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2775 time to fit residues: 87.6997 Evaluate side-chains 162 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 156 optimal weight: 0.0570 chunk 186 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN D 651 ASN F 652 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050405 restraints weight = 69476.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052316 restraints weight = 39997.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053654 restraints weight = 27686.191| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17044 Z= 0.120 Angle : 0.685 19.036 23339 Z= 0.322 Chirality : 0.048 0.424 2879 Planarity : 0.004 0.051 2788 Dihedral : 7.721 67.980 4217 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1894 helix: 0.22 (0.26), residues: 420 sheet: -0.04 (0.22), residues: 562 loop : -0.53 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 69 HIS 0.010 0.001 HIS A 249 PHE 0.012 0.001 PHE E 233 TYR 0.012 0.001 TYR A 191 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 55) link_NAG-ASN : angle 2.96866 ( 165) link_ALPHA1-6 : bond 0.00605 ( 7) link_ALPHA1-6 : angle 1.76017 ( 21) link_BETA1-4 : bond 0.00694 ( 34) link_BETA1-4 : angle 2.26161 ( 102) link_ALPHA1-3 : bond 0.00909 ( 7) link_ALPHA1-3 : angle 2.23979 ( 21) hydrogen bonds : bond 0.03954 ( 460) hydrogen bonds : angle 5.05246 ( 1200) SS BOND : bond 0.00266 ( 34) SS BOND : angle 0.88754 ( 68) covalent geometry : bond 0.00256 (16905) covalent geometry : angle 0.61683 (22962) Misc. bond : bond 0.00382 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.730 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 180 ASP cc_start: 0.8830 (m-30) cc_final: 0.8572 (m-30) REVERT: A 374 HIS cc_start: 0.7837 (t-170) cc_final: 0.7490 (t-90) REVERT: A 434 MET cc_start: 0.8993 (ptp) cc_final: 0.8668 (ptp) REVERT: C 53 PHE cc_start: 0.8364 (m-80) cc_final: 0.7713 (m-80) REVERT: C 69 TRP cc_start: 0.8875 (m-90) cc_final: 0.7725 (m-10) REVERT: C 104 MET cc_start: 0.9301 (tmm) cc_final: 0.9067 (tmm) REVERT: C 111 LEU cc_start: 0.9423 (mm) cc_final: 0.9074 (mt) REVERT: C 210 PHE cc_start: 0.9011 (m-80) cc_final: 0.8633 (m-10) REVERT: C 260 LEU cc_start: 0.9165 (mt) cc_final: 0.8894 (mt) REVERT: D 584 GLU cc_start: 0.9238 (tp30) cc_final: 0.8399 (tm-30) REVERT: D 655 LYS cc_start: 0.8956 (mmpt) cc_final: 0.8729 (ptpp) REVERT: D 657 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8370 (mt-10) REVERT: E 95 MET cc_start: 0.8541 (mmp) cc_final: 0.8103 (mmm) REVERT: E 180 ASP cc_start: 0.8930 (m-30) cc_final: 0.8247 (m-30) REVERT: F 576 LEU cc_start: 0.8566 (mt) cc_final: 0.8002 (tt) REVERT: F 584 GLU cc_start: 0.8569 (tp30) cc_final: 0.7976 (tm-30) REVERT: F 601 LYS cc_start: 0.8895 (tptt) cc_final: 0.8287 (tppp) REVERT: F 630 GLN cc_start: 0.9291 (mt0) cc_final: 0.8929 (mt0) REVERT: F 647 GLU cc_start: 0.8397 (pt0) cc_final: 0.7955 (pt0) REVERT: B 540 GLN cc_start: 0.9193 (mm110) cc_final: 0.8850 (mm-40) REVERT: B 591 GLN cc_start: 0.9259 (tp40) cc_final: 0.8857 (tp40) REVERT: B 607 ASN cc_start: 0.8043 (m-40) cc_final: 0.7837 (m-40) REVERT: B 633 LYS cc_start: 0.9475 (mttt) cc_final: 0.9229 (mtmt) REVERT: L 53 ASN cc_start: 0.8617 (m-40) cc_final: 0.8110 (t0) REVERT: L 91 TYR cc_start: 0.7592 (t80) cc_final: 0.7384 (t80) REVERT: H 67 PHE cc_start: 0.8173 (m-10) cc_final: 0.7906 (m-10) REVERT: H 83 ARG cc_start: 0.8537 (mpp80) cc_final: 0.8193 (mpp80) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2598 time to fit residues: 88.0600 Evaluate side-chains 167 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 172 optimal weight: 30.0000 chunk 149 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN E 85 HIS E 246 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049784 restraints weight = 70565.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.051626 restraints weight = 41344.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052922 restraints weight = 29041.888| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17044 Z= 0.143 Angle : 0.680 18.545 23339 Z= 0.321 Chirality : 0.047 0.413 2879 Planarity : 0.004 0.055 2788 Dihedral : 7.466 68.178 4217 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % 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: -0.35 (0.20), residues: 1894 helix: 0.38 (0.27), residues: 417 sheet: -0.03 (0.22), residues: 562 loop : -0.56 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 69 HIS 0.008 0.001 HIS E 85 PHE 0.025 0.001 PHE E 233 TYR 0.012 0.001 TYR E 484 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 55) link_NAG-ASN : angle 2.93114 ( 165) link_ALPHA1-6 : bond 0.00587 ( 7) link_ALPHA1-6 : angle 1.72307 ( 21) link_BETA1-4 : bond 0.00610 ( 34) link_BETA1-4 : angle 2.25031 ( 102) link_ALPHA1-3 : bond 0.00803 ( 7) link_ALPHA1-3 : angle 2.26886 ( 21) hydrogen bonds : bond 0.03946 ( 460) hydrogen bonds : angle 5.05875 ( 1200) SS BOND : bond 0.00288 ( 34) SS BOND : angle 0.87804 ( 68) covalent geometry : bond 0.00316 (16905) covalent geometry : angle 0.61344 (22962) Misc. bond : bond 0.00421 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8841 (m-30) cc_final: 0.8640 (m-30) REVERT: A 374 HIS cc_start: 0.7755 (t-170) cc_final: 0.7490 (t-90) REVERT: A 434 MET cc_start: 0.9164 (ptp) cc_final: 0.8736 (ptp) REVERT: C 53 PHE cc_start: 0.8304 (m-80) cc_final: 0.7880 (m-80) REVERT: C 69 TRP cc_start: 0.8903 (m-90) cc_final: 0.7757 (m-10) REVERT: C 104 MET cc_start: 0.9337 (tmm) cc_final: 0.9029 (tmm) REVERT: C 111 LEU cc_start: 0.9393 (mm) cc_final: 0.9056 (mt) REVERT: C 116 LEU cc_start: 0.9355 (tt) cc_final: 0.9123 (mp) REVERT: C 210 PHE cc_start: 0.8912 (m-80) cc_final: 0.8611 (m-10) REVERT: C 260 LEU cc_start: 0.9128 (mt) cc_final: 0.8851 (mt) REVERT: D 584 GLU cc_start: 0.9153 (tp30) cc_final: 0.8343 (tm-30) REVERT: D 590 GLN cc_start: 0.9364 (tp40) cc_final: 0.8982 (tp40) REVERT: D 657 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8460 (mt-10) REVERT: E 180 ASP cc_start: 0.8920 (m-30) cc_final: 0.8256 (m-30) REVERT: E 479 TRP cc_start: 0.8533 (m-90) cc_final: 0.8170 (m-90) REVERT: F 576 LEU cc_start: 0.8584 (mt) cc_final: 0.7999 (tt) REVERT: F 584 GLU cc_start: 0.8544 (tp30) cc_final: 0.7973 (tm-30) REVERT: F 601 LYS cc_start: 0.8907 (tptt) cc_final: 0.8311 (tppp) REVERT: F 625 ASN cc_start: 0.8670 (t0) cc_final: 0.8432 (t0) REVERT: F 647 GLU cc_start: 0.8386 (pt0) cc_final: 0.7954 (pt0) REVERT: B 540 GLN cc_start: 0.9126 (mm110) cc_final: 0.8153 (mt0) REVERT: B 591 GLN cc_start: 0.9283 (tp40) cc_final: 0.9070 (tp40) REVERT: B 607 ASN cc_start: 0.8061 (m-40) cc_final: 0.7859 (m-40) REVERT: B 659 ASP cc_start: 0.9114 (m-30) cc_final: 0.8751 (p0) REVERT: L 49 TYR cc_start: 0.8966 (p90) cc_final: 0.7992 (p90) REVERT: L 53 ASN cc_start: 0.8607 (m-40) cc_final: 0.8156 (t0) REVERT: L 91 TYR cc_start: 0.7625 (t80) cc_final: 0.7405 (t80) REVERT: H 13 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8369 (mm-40) REVERT: H 28 THR cc_start: 0.8783 (m) cc_final: 0.8529 (p) REVERT: H 67 PHE cc_start: 0.8247 (m-10) cc_final: 0.7992 (m-10) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2620 time to fit residues: 86.0962 Evaluate side-chains 163 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3254 r_free = 0.3254 target = 0.065809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049368 restraints weight = 71044.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051195 restraints weight = 41544.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052463 restraints weight = 29188.899| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17044 Z= 0.163 Angle : 0.720 18.458 23339 Z= 0.340 Chirality : 0.048 0.406 2879 Planarity : 0.004 0.057 2788 Dihedral : 7.398 68.373 4217 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1894 helix: 0.30 (0.27), residues: 420 sheet: -0.10 (0.22), residues: 553 loop : -0.60 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 PHE 0.026 0.001 PHE E 233 TYR 0.011 0.001 TYR E 484 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 55) link_NAG-ASN : angle 3.00079 ( 165) link_ALPHA1-6 : bond 0.00577 ( 7) link_ALPHA1-6 : angle 1.72582 ( 21) link_BETA1-4 : bond 0.00601 ( 34) link_BETA1-4 : angle 2.22972 ( 102) link_ALPHA1-3 : bond 0.00804 ( 7) link_ALPHA1-3 : angle 2.26721 ( 21) hydrogen bonds : bond 0.03917 ( 460) hydrogen bonds : angle 5.07402 ( 1200) SS BOND : bond 0.00358 ( 34) SS BOND : angle 2.21205 ( 68) covalent geometry : bond 0.00367 (16905) covalent geometry : angle 0.64636 (22962) Misc. bond : bond 0.00370 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.715 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 434 MET cc_start: 0.9095 (ptp) cc_final: 0.8617 (ptp) REVERT: C 53 PHE cc_start: 0.8329 (m-80) cc_final: 0.7934 (m-80) REVERT: C 104 MET cc_start: 0.9371 (tmm) cc_final: 0.9030 (tmm) REVERT: C 111 LEU cc_start: 0.9418 (mm) cc_final: 0.9065 (mt) REVERT: C 210 PHE cc_start: 0.9012 (m-80) cc_final: 0.8718 (m-10) REVERT: C 260 LEU cc_start: 0.9164 (mt) cc_final: 0.8911 (mt) REVERT: D 584 GLU cc_start: 0.9182 (tp30) cc_final: 0.8367 (tm-30) REVERT: D 590 GLN cc_start: 0.9367 (tp40) cc_final: 0.8993 (tp40) REVERT: D 657 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8590 (mt-10) REVERT: E 180 ASP cc_start: 0.8940 (m-30) cc_final: 0.8292 (m-30) REVERT: E 226 LEU cc_start: 0.9285 (mt) cc_final: 0.9038 (mt) REVERT: E 479 TRP cc_start: 0.8546 (m-90) cc_final: 0.8121 (m-90) REVERT: F 576 LEU cc_start: 0.8566 (mt) cc_final: 0.7984 (tt) REVERT: F 584 GLU cc_start: 0.8572 (tp30) cc_final: 0.8001 (tm-30) REVERT: F 601 LYS cc_start: 0.8907 (tptt) cc_final: 0.8334 (tppp) REVERT: F 625 ASN cc_start: 0.8699 (t0) cc_final: 0.8480 (t0) REVERT: F 647 GLU cc_start: 0.8403 (pt0) cc_final: 0.7983 (pt0) REVERT: B 540 GLN cc_start: 0.9119 (mm110) cc_final: 0.8728 (mm-40) REVERT: B 591 GLN cc_start: 0.9306 (tp40) cc_final: 0.9086 (tp40) REVERT: B 601 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8691 (mmmm) REVERT: B 607 ASN cc_start: 0.8070 (m-40) cc_final: 0.7863 (m-40) REVERT: B 659 ASP cc_start: 0.9126 (m-30) cc_final: 0.8770 (p0) REVERT: L 4 LEU cc_start: 0.7661 (mm) cc_final: 0.7454 (mt) REVERT: L 49 TYR cc_start: 0.8958 (p90) cc_final: 0.8711 (p90) REVERT: L 91 TYR cc_start: 0.7539 (t80) cc_final: 0.6846 (t80) REVERT: H 13 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8438 (mm-40) REVERT: H 28 THR cc_start: 0.8716 (m) cc_final: 0.8470 (p) REVERT: H 67 PHE cc_start: 0.8313 (m-10) cc_final: 0.8109 (m-10) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2722 time to fit residues: 85.3102 Evaluate side-chains 156 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049939 restraints weight = 71106.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051779 restraints weight = 41523.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053067 restraints weight = 29165.656| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17044 Z= 0.138 Angle : 0.693 18.456 23339 Z= 0.330 Chirality : 0.048 0.405 2879 Planarity : 0.004 0.057 2788 Dihedral : 7.222 68.773 4217 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 (0.20), residues: 1894 helix: 0.25 (0.27), residues: 420 sheet: -0.08 (0.22), residues: 553 loop : -0.57 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 69 HIS 0.014 0.001 HIS A 374 PHE 0.024 0.001 PHE E 233 TYR 0.015 0.001 TYR H 100R ARG 0.007 0.000 ARG C 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 55) link_NAG-ASN : angle 2.89717 ( 165) link_ALPHA1-6 : bond 0.00606 ( 7) link_ALPHA1-6 : angle 1.68145 ( 21) link_BETA1-4 : bond 0.00623 ( 34) link_BETA1-4 : angle 2.15804 ( 102) link_ALPHA1-3 : bond 0.00824 ( 7) link_ALPHA1-3 : angle 2.17548 ( 21) hydrogen bonds : bond 0.03881 ( 460) hydrogen bonds : angle 5.04187 ( 1200) SS BOND : bond 0.00356 ( 34) SS BOND : angle 1.71689 ( 68) covalent geometry : bond 0.00308 (16905) covalent geometry : angle 0.62548 (22962) Misc. bond : bond 0.00415 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.834 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 374 HIS cc_start: 0.8024 (t-90) cc_final: 0.7292 (t-90) REVERT: A 434 MET cc_start: 0.9033 (ptp) cc_final: 0.8566 (ptp) REVERT: C 53 PHE cc_start: 0.8267 (m-80) cc_final: 0.7920 (m-80) REVERT: C 111 LEU cc_start: 0.9392 (mm) cc_final: 0.9054 (mt) REVERT: C 116 LEU cc_start: 0.9396 (tt) cc_final: 0.9141 (mp) REVERT: C 207 LYS cc_start: 0.8478 (pttt) cc_final: 0.8144 (tptt) REVERT: C 210 PHE cc_start: 0.9004 (m-80) cc_final: 0.8730 (m-10) REVERT: C 260 LEU cc_start: 0.9120 (mt) cc_final: 0.8881 (mt) REVERT: C 477 ASP cc_start: 0.8569 (m-30) cc_final: 0.7859 (p0) REVERT: D 530 MET cc_start: 0.6933 (tpp) cc_final: 0.5969 (tpp) REVERT: D 584 GLU cc_start: 0.9152 (tp30) cc_final: 0.8330 (tm-30) REVERT: D 590 GLN cc_start: 0.9357 (tp40) cc_final: 0.8962 (tp40) REVERT: D 648 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8511 (pp20) REVERT: D 657 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8490 (mt-10) REVERT: E 180 ASP cc_start: 0.8939 (m-30) cc_final: 0.8131 (m-30) REVERT: E 226 LEU cc_start: 0.9236 (mt) cc_final: 0.8941 (mt) REVERT: E 479 TRP cc_start: 0.8509 (m-90) cc_final: 0.8299 (m-90) REVERT: F 576 LEU cc_start: 0.8564 (mt) cc_final: 0.7994 (tt) REVERT: F 584 GLU cc_start: 0.8548 (tp30) cc_final: 0.7967 (tm-30) REVERT: F 601 LYS cc_start: 0.8902 (tptt) cc_final: 0.8346 (tppp) REVERT: F 625 ASN cc_start: 0.8720 (t0) cc_final: 0.8493 (t0) REVERT: F 647 GLU cc_start: 0.8375 (pt0) cc_final: 0.7992 (pt0) REVERT: B 536 THR cc_start: 0.9184 (p) cc_final: 0.8978 (p) REVERT: B 540 GLN cc_start: 0.9155 (mm110) cc_final: 0.8737 (mm-40) REVERT: B 591 GLN cc_start: 0.9271 (tp40) cc_final: 0.9065 (tp40) REVERT: B 630 GLN cc_start: 0.9220 (mt0) cc_final: 0.8573 (mt0) REVERT: B 659 ASP cc_start: 0.9200 (m-30) cc_final: 0.8766 (p0) REVERT: L 53 ASN cc_start: 0.8962 (m110) cc_final: 0.8657 (m110) REVERT: L 75 ILE cc_start: 0.8550 (mt) cc_final: 0.8208 (tt) REVERT: L 82 ASP cc_start: 0.6430 (m-30) cc_final: 0.5438 (m-30) REVERT: L 91 TYR cc_start: 0.7154 (t80) cc_final: 0.6613 (t80) REVERT: L 106 VAL cc_start: 0.4958 (m) cc_final: 0.4741 (t) REVERT: H 13 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8502 (mm-40) REVERT: H 100 TYR cc_start: 0.9036 (m-80) cc_final: 0.8821 (m-80) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2722 time to fit residues: 87.6879 Evaluate side-chains 157 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 28 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 348 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.062969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.046462 restraints weight = 74068.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.048174 restraints weight = 43825.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049378 restraints weight = 31119.278| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17044 Z= 0.310 Angle : 0.870 18.023 23339 Z= 0.418 Chirality : 0.050 0.403 2879 Planarity : 0.005 0.055 2788 Dihedral : 7.872 70.546 4217 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.91 (0.19), residues: 1894 helix: -0.00 (0.26), residues: 408 sheet: -0.45 (0.22), residues: 550 loop : -0.88 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 427 HIS 0.019 0.002 HIS A 374 PHE 0.037 0.002 PHE E 233 TYR 0.020 0.002 TYR E 384 ARG 0.010 0.001 ARG C 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 55) link_NAG-ASN : angle 3.08900 ( 165) link_ALPHA1-6 : bond 0.00521 ( 7) link_ALPHA1-6 : angle 1.79490 ( 21) link_BETA1-4 : bond 0.00596 ( 34) link_BETA1-4 : angle 2.44642 ( 102) link_ALPHA1-3 : bond 0.00703 ( 7) link_ALPHA1-3 : angle 2.46290 ( 21) hydrogen bonds : bond 0.04499 ( 460) hydrogen bonds : angle 5.52540 ( 1200) SS BOND : bond 0.00536 ( 34) SS BOND : angle 1.89969 ( 68) covalent geometry : bond 0.00685 (16905) covalent geometry : angle 0.80954 (22962) Misc. bond : bond 0.00251 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4687.13 seconds wall clock time: 82 minutes 42.06 seconds (4962.06 seconds total)