Starting phenix.real_space_refine on Thu Sep 18 12:48:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t76_25735/09_2025/7t76_25735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t76_25735/09_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_25735/09_2025/7t76_25735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t76_25735/09_2025/7t76_25735.map" model { file = "/net/cci-nas-00/data/ceres_data/7t76_25735/09_2025/7t76_25735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t76_25735/09_2025/7t76_25735.cif" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.39, per 1000 atoms: 0.20 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: 1.89 Conformation dependent library (CDL) restraints added in 706.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 2.17 Time building geometry restraints manager: 2.38 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 605) selection = (chain 'E' and resid 32 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.240 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 192 TYR 0.058 0.008 TYR C 40 PHE 0.032 0.006 PHE E 233 TRP 0.050 0.010 TRP E 96 HIS 0.017 0.003 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.02162 (16905) covalent geometry : angle 1.96917 (22962) SS BOND : bond 0.05257 ( 34) SS BOND : angle 3.45474 ( 68) hydrogen bonds : bond 0.17061 ( 460) hydrogen bonds : angle 7.63151 ( 1200) Misc. bond : bond 0.90660 ( 2) link_ALPHA1-3 : bond 0.00409 ( 7) link_ALPHA1-3 : angle 2.62497 ( 21) 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_NAG-ASN : bond 0.07423 ( 55) link_NAG-ASN : angle 3.16228 ( 165) *********************** 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 : 0.474 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: 0.1378 time to fit residues: 91.2304 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053098 restraints weight = 68331.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055140 restraints weight = 39262.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056572 restraints weight = 27099.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057560 restraints weight = 20986.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058135 restraints weight = 17557.332| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17044 Z= 0.176 Angle : 0.885 21.279 23339 Z= 0.414 Chirality : 0.053 0.655 2879 Planarity : 0.004 0.049 2788 Dihedral : 11.424 79.914 4217 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.19), residues: 1894 helix: 0.19 (0.26), residues: 417 sheet: 0.42 (0.22), residues: 522 loop : -0.21 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 273 TYR 0.016 0.002 TYR E 435 PHE 0.039 0.002 PHE E 233 TRP 0.029 0.002 TRP C 96 HIS 0.007 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00377 (16905) covalent geometry : angle 0.78679 (22962) SS BOND : bond 0.00385 ( 34) SS BOND : angle 1.34150 ( 68) hydrogen bonds : bond 0.05831 ( 460) hydrogen bonds : angle 5.97880 ( 1200) Misc. bond : bond 0.00386 ( 2) link_ALPHA1-3 : bond 0.00711 ( 7) link_ALPHA1-3 : angle 2.54329 ( 21) link_ALPHA1-6 : bond 0.00526 ( 7) link_ALPHA1-6 : angle 1.75828 ( 21) link_BETA1-4 : bond 0.00848 ( 34) link_BETA1-4 : angle 3.33640 ( 102) link_NAG-ASN : bond 0.00651 ( 55) link_NAG-ASN : angle 3.96954 ( 165) *********************** 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 308 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.659 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: A 98 ASN cc_start: 0.8570 (t0) cc_final: 0.7501 (m-40) REVERT: A 181 ILE cc_start: 0.9450 (pt) cc_final: 0.8982 (mm) REVERT: A 374 HIS cc_start: 0.7706 (t-170) cc_final: 0.7429 (t-90) REVERT: C 53 PHE cc_start: 0.8294 (m-80) cc_final: 0.7987 (m-80) REVERT: C 69 TRP cc_start: 0.8581 (m-90) cc_final: 0.8102 (m-10) REVERT: C 111 LEU cc_start: 0.9467 (mm) cc_final: 0.9063 (mt) REVERT: C 122 LEU cc_start: 0.9511 (mt) cc_final: 0.9305 (mm) REVERT: C 136 ASN cc_start: 0.6421 (t0) cc_final: 0.6161 (m110) REVERT: C 210 PHE cc_start: 0.8615 (m-80) cc_final: 0.8097 (m-10) REVERT: C 260 LEU cc_start: 0.9263 (mt) cc_final: 0.9031 (mt) REVERT: C 416 LEU cc_start: 0.8862 (mt) cc_final: 0.8459 (pp) REVERT: D 584 GLU cc_start: 0.8997 (tp30) cc_final: 0.8152 (tm-30) REVERT: D 607 ASN cc_start: 0.8415 (m110) cc_final: 0.8066 (p0) REVERT: D 657 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8580 (mp0) REVERT: E 180 ASP cc_start: 0.8676 (m-30) cc_final: 0.8298 (m-30) REVERT: E 315 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8880 (mp10) REVERT: F 574 LYS cc_start: 0.6595 (pttm) cc_final: 0.6047 (mmpt) REVERT: F 607 ASN cc_start: 0.8416 (m-40) cc_final: 0.7977 (p0) REVERT: F 647 GLU cc_start: 0.8351 (pt0) cc_final: 0.7780 (pt0) REVERT: B 530 MET cc_start: 0.8204 (mtp) cc_final: 0.8003 (ppp) REVERT: B 538 THR cc_start: 0.9098 (t) cc_final: 0.8878 (t) REVERT: B 584 GLU cc_start: 0.8616 (tt0) cc_final: 0.8151 (tp30) REVERT: B 632 ASP cc_start: 0.9147 (t0) cc_final: 0.8841 (p0) REVERT: B 643 TYR cc_start: 0.8674 (m-10) cc_final: 0.8014 (m-10) REVERT: L 73 LEU cc_start: 0.9287 (tp) cc_final: 0.9039 (tp) REVERT: L 91 TYR cc_start: 0.8022 (t80) cc_final: 0.7587 (t80) REVERT: L 104 LEU cc_start: 0.7701 (tt) cc_final: 0.6609 (tp) REVERT: H 68 THR cc_start: 0.8762 (m) cc_final: 0.8439 (t) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1273 time to fit residues: 60.5225 Evaluate side-chains 196 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 114 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051173 restraints weight = 70174.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053105 restraints weight = 40898.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054464 restraints weight = 28506.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055417 restraints weight = 22289.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056033 restraints weight = 18762.994| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17044 Z= 0.172 Angle : 0.774 19.450 23339 Z= 0.363 Chirality : 0.049 0.476 2879 Planarity : 0.005 0.150 2788 Dihedral : 9.778 70.374 4217 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1894 helix: 0.44 (0.27), residues: 390 sheet: 0.22 (0.21), residues: 557 loop : -0.25 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 19 TYR 0.021 0.001 TYR E 484 PHE 0.046 0.002 PHE E 233 TRP 0.042 0.002 TRP H 36 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00376 (16905) covalent geometry : angle 0.69284 (22962) SS BOND : bond 0.00360 ( 34) SS BOND : angle 1.06697 ( 68) hydrogen bonds : bond 0.04622 ( 460) hydrogen bonds : angle 5.56071 ( 1200) Misc. bond : bond 0.00568 ( 2) link_ALPHA1-3 : bond 0.00814 ( 7) link_ALPHA1-3 : angle 2.33573 ( 21) link_ALPHA1-6 : bond 0.00471 ( 7) link_ALPHA1-6 : angle 1.77198 ( 21) link_BETA1-4 : bond 0.00723 ( 34) link_BETA1-4 : angle 2.80001 ( 102) link_NAG-ASN : bond 0.00565 ( 55) link_NAG-ASN : angle 3.39022 ( 165) *********************** 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 251 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.586 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: A 104 MET cc_start: 0.9244 (ttt) cc_final: 0.9005 (ttm) REVERT: A 286 VAL cc_start: 0.9441 (t) cc_final: 0.9024 (p) REVERT: A 374 HIS cc_start: 0.7736 (t-170) cc_final: 0.7477 (t-90) REVERT: C 53 PHE cc_start: 0.8394 (m-80) cc_final: 0.8088 (m-80) REVERT: C 69 TRP cc_start: 0.8647 (m-90) cc_final: 0.8028 (m-10) REVERT: C 111 LEU cc_start: 0.9466 (mm) cc_final: 0.9036 (mt) REVERT: C 122 LEU cc_start: 0.9562 (mt) cc_final: 0.9351 (mm) REVERT: C 136 ASN cc_start: 0.6688 (t0) cc_final: 0.6376 (m110) REVERT: C 210 PHE cc_start: 0.8692 (m-80) cc_final: 0.8192 (m-10) REVERT: C 260 LEU cc_start: 0.9263 (mt) cc_final: 0.9062 (mt) REVERT: C 477 ASP cc_start: 0.8579 (m-30) cc_final: 0.8241 (p0) REVERT: D 584 GLU cc_start: 0.9203 (tp30) cc_final: 0.8220 (tm-30) REVERT: D 607 ASN cc_start: 0.8370 (m110) cc_final: 0.8054 (p0) REVERT: D 648 GLU cc_start: 0.8686 (pp20) cc_final: 0.8026 (pp20) REVERT: D 657 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8382 (mp0) REVERT: E 180 ASP cc_start: 0.8767 (m-30) cc_final: 0.8258 (m-30) REVERT: E 315 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8892 (mp10) REVERT: F 574 LYS cc_start: 0.7506 (pttm) cc_final: 0.7155 (mmpt) REVERT: F 576 LEU cc_start: 0.8687 (mt) cc_final: 0.8037 (tt) REVERT: F 606 THR cc_start: 0.8881 (p) cc_final: 0.8479 (t) REVERT: F 607 ASN cc_start: 0.8544 (m-40) cc_final: 0.7992 (p0) REVERT: F 647 GLU cc_start: 0.8457 (pt0) cc_final: 0.8091 (pt0) REVERT: B 540 GLN cc_start: 0.9153 (mm110) cc_final: 0.8061 (mt0) REVERT: B 584 GLU cc_start: 0.8673 (tt0) cc_final: 0.8184 (tp30) REVERT: B 591 GLN cc_start: 0.9321 (tp40) cc_final: 0.8916 (tp40) REVERT: B 601 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8694 (mmmm) REVERT: B 643 TYR cc_start: 0.8736 (m-10) cc_final: 0.8007 (m-10) REVERT: L 49 TYR cc_start: 0.8972 (p90) cc_final: 0.8204 (p90) REVERT: L 53 ASN cc_start: 0.8647 (m-40) cc_final: 0.7940 (t0) REVERT: L 73 LEU cc_start: 0.9297 (tp) cc_final: 0.9001 (tp) REVERT: L 91 TYR cc_start: 0.7898 (t80) cc_final: 0.7513 (t80) REVERT: H 68 THR cc_start: 0.8717 (m) cc_final: 0.8338 (t) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1220 time to fit residues: 47.6941 Evaluate side-chains 183 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.0170 chunk 155 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 591 GLN F 652 GLN B 658 GLN L 17 GLN L 37 GLN L 39 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052168 restraints weight = 69078.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054129 restraints weight = 39959.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055487 restraints weight = 27716.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056446 restraints weight = 21636.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057097 restraints weight = 18191.767| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17044 Z= 0.125 Angle : 0.704 19.354 23339 Z= 0.329 Chirality : 0.048 0.451 2879 Planarity : 0.004 0.117 2788 Dihedral : 8.956 65.471 4217 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1894 helix: 0.43 (0.27), residues: 390 sheet: 0.33 (0.21), residues: 566 loop : -0.33 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.015 0.001 TYR E 384 PHE 0.040 0.001 PHE E 233 TRP 0.023 0.002 TRP A 69 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00269 (16905) covalent geometry : angle 0.62600 (22962) SS BOND : bond 0.00290 ( 34) SS BOND : angle 1.00492 ( 68) hydrogen bonds : bond 0.04094 ( 460) hydrogen bonds : angle 5.26746 ( 1200) Misc. bond : bond 0.00514 ( 2) link_ALPHA1-3 : bond 0.00881 ( 7) link_ALPHA1-3 : angle 2.29919 ( 21) link_ALPHA1-6 : bond 0.00506 ( 7) link_ALPHA1-6 : angle 1.70006 ( 21) link_BETA1-4 : bond 0.00724 ( 34) link_BETA1-4 : angle 2.57012 ( 102) link_NAG-ASN : bond 0.00578 ( 55) link_NAG-ASN : angle 3.15358 ( 165) *********************** 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 249 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.694 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 69 TRP cc_start: 0.8581 (m-10) cc_final: 0.7808 (m-10) REVERT: A 180 ASP cc_start: 0.8822 (m-30) cc_final: 0.8158 (m-30) REVERT: A 374 HIS cc_start: 0.7751 (t-170) cc_final: 0.7522 (t-90) REVERT: A 494 LEU cc_start: 0.8757 (tt) cc_final: 0.8489 (tt) REVERT: C 53 PHE cc_start: 0.8445 (m-80) cc_final: 0.8056 (m-80) REVERT: C 69 TRP cc_start: 0.8686 (m-90) cc_final: 0.8068 (m-10) REVERT: C 86 LEU cc_start: 0.8697 (mm) cc_final: 0.8429 (mt) REVERT: C 111 LEU cc_start: 0.9397 (mm) cc_final: 0.9021 (mt) REVERT: C 116 LEU cc_start: 0.9330 (tt) cc_final: 0.8917 (mp) REVERT: C 136 ASN cc_start: 0.6732 (t0) cc_final: 0.6439 (m110) REVERT: C 210 PHE cc_start: 0.8630 (m-80) cc_final: 0.8250 (m-10) REVERT: C 477 ASP cc_start: 0.8584 (m-30) cc_final: 0.7980 (p0) REVERT: D 537 LEU cc_start: 0.9347 (mt) cc_final: 0.9082 (mm) REVERT: D 584 GLU cc_start: 0.9145 (tp30) cc_final: 0.8196 (tm-30) REVERT: D 607 ASN cc_start: 0.8248 (m-40) cc_final: 0.7948 (p0) REVERT: D 648 GLU cc_start: 0.8819 (pp20) cc_final: 0.8570 (pp20) REVERT: E 180 ASP cc_start: 0.8813 (m-30) cc_final: 0.8220 (m-30) REVERT: E 315 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8800 (mp10) REVERT: F 574 LYS cc_start: 0.7450 (pttm) cc_final: 0.7051 (mmpt) REVERT: F 576 LEU cc_start: 0.8612 (mt) cc_final: 0.8042 (tt) REVERT: F 606 THR cc_start: 0.8646 (p) cc_final: 0.8310 (t) REVERT: F 607 ASN cc_start: 0.8329 (m-40) cc_final: 0.7645 (p0) REVERT: F 622 ILE cc_start: 0.9258 (pt) cc_final: 0.8992 (pt) REVERT: F 647 GLU cc_start: 0.8514 (pt0) cc_final: 0.8113 (pt0) REVERT: B 540 GLN cc_start: 0.9150 (mm110) cc_final: 0.8033 (mt0) REVERT: B 584 GLU cc_start: 0.8721 (tt0) cc_final: 0.8043 (tp30) REVERT: B 602 LEU cc_start: 0.9393 (mm) cc_final: 0.9186 (mm) REVERT: B 643 TYR cc_start: 0.8856 (m-10) cc_final: 0.8487 (m-10) REVERT: L 49 TYR cc_start: 0.9132 (p90) cc_final: 0.8839 (p90) REVERT: L 53 ASN cc_start: 0.9047 (m-40) cc_final: 0.8687 (t0) REVERT: L 91 TYR cc_start: 0.7760 (t80) cc_final: 0.7426 (t80) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.1109 time to fit residues: 44.0601 Evaluate side-chains 177 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN E 478 ASN F 585 HIS F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS H 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.063740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.047198 restraints weight = 72183.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.048983 restraints weight = 42348.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050201 restraints weight = 29887.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051069 restraints weight = 23677.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.051564 restraints weight = 20164.743| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17044 Z= 0.294 Angle : 0.855 18.390 23339 Z= 0.403 Chirality : 0.050 0.436 2879 Planarity : 0.005 0.052 2788 Dihedral : 8.736 65.255 4217 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.19), residues: 1894 helix: 0.13 (0.26), residues: 402 sheet: -0.17 (0.21), residues: 575 loop : -0.64 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 298 TYR 0.015 0.002 TYR E 384 PHE 0.036 0.002 PHE E 233 TRP 0.023 0.003 TRP A 479 HIS 0.009 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00642 (16905) covalent geometry : angle 0.78968 (22962) SS BOND : bond 0.00567 ( 34) SS BOND : angle 1.22825 ( 68) hydrogen bonds : bond 0.04601 ( 460) hydrogen bonds : angle 5.50642 ( 1200) Misc. bond : bond 0.00349 ( 2) link_ALPHA1-3 : bond 0.00744 ( 7) link_ALPHA1-3 : angle 2.67185 ( 21) link_ALPHA1-6 : bond 0.00538 ( 7) link_ALPHA1-6 : angle 1.93349 ( 21) link_BETA1-4 : bond 0.00606 ( 34) link_BETA1-4 : angle 2.68273 ( 102) link_NAG-ASN : bond 0.00602 ( 55) link_NAG-ASN : angle 3.19487 ( 165) *********************** 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 209 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8553 (m-10) cc_final: 0.8136 (m-10) REVERT: A 104 MET cc_start: 0.9347 (ttm) cc_final: 0.9052 (ttm) REVERT: A 180 ASP cc_start: 0.8896 (m-30) cc_final: 0.8327 (m-30) REVERT: C 53 PHE cc_start: 0.8561 (m-80) cc_final: 0.8018 (m-80) REVERT: C 69 TRP cc_start: 0.8858 (m-90) cc_final: 0.7740 (m-10) REVERT: C 104 MET cc_start: 0.9333 (tmm) cc_final: 0.9088 (tmm) REVERT: C 111 LEU cc_start: 0.9477 (mm) cc_final: 0.9026 (mt) REVERT: C 136 ASN cc_start: 0.6809 (t0) cc_final: 0.6494 (m110) REVERT: C 207 LYS cc_start: 0.8406 (pttt) cc_final: 0.8194 (tptt) REVERT: C 260 LEU cc_start: 0.9417 (mt) cc_final: 0.9162 (mt) REVERT: D 584 GLU cc_start: 0.9196 (tp30) cc_final: 0.8332 (tm-30) REVERT: D 590 GLN cc_start: 0.9319 (tp40) cc_final: 0.8880 (tp40) REVERT: E 92 GLU cc_start: 0.8780 (tt0) cc_final: 0.8511 (tt0) REVERT: E 98 ASN cc_start: 0.8922 (t0) cc_final: 0.8688 (t0) REVERT: E 180 ASP cc_start: 0.8902 (m-30) cc_final: 0.8364 (m-30) REVERT: F 576 LEU cc_start: 0.8705 (mt) cc_final: 0.8078 (tt) REVERT: F 584 GLU cc_start: 0.8607 (tp30) cc_final: 0.8012 (tm-30) REVERT: F 591 GLN cc_start: 0.9539 (tt0) cc_final: 0.8979 (tt0) REVERT: F 622 ILE cc_start: 0.9129 (pt) cc_final: 0.8927 (pt) REVERT: F 647 GLU cc_start: 0.8471 (pt0) cc_final: 0.8092 (pt0) REVERT: F 652 GLN cc_start: 0.8295 (tp40) cc_final: 0.7965 (tp-100) REVERT: B 591 GLN cc_start: 0.9375 (tp40) cc_final: 0.8939 (tp40) REVERT: B 601 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8684 (mmmm) REVERT: B 607 ASN cc_start: 0.8473 (m-40) cc_final: 0.8262 (m-40) REVERT: L 49 TYR cc_start: 0.9219 (p90) cc_final: 0.8462 (p90) REVERT: L 53 ASN cc_start: 0.9058 (m-40) cc_final: 0.8535 (t0) REVERT: L 91 TYR cc_start: 0.7783 (t80) cc_final: 0.7402 (t80) REVERT: H 13 GLN cc_start: 0.8820 (mm110) cc_final: 0.8399 (mm-40) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1222 time to fit residues: 40.1220 Evaluate side-chains 151 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 178 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 478 ASN D 652 GLN D 656 ASN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN L 17 GLN 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 = 0.3265 r_free = 0.3265 target = 0.066387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.049853 restraints weight = 69541.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.051761 restraints weight = 39833.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.053089 restraints weight = 27544.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054017 restraints weight = 21528.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054650 restraints weight = 18171.866| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17044 Z= 0.129 Angle : 0.712 19.072 23339 Z= 0.332 Chirality : 0.049 0.411 2879 Planarity : 0.004 0.050 2788 Dihedral : 8.097 68.173 4217 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 0.06 % Allowed : 0.94 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.19), residues: 1894 helix: 0.04 (0.25), residues: 426 sheet: -0.00 (0.21), residues: 566 loop : -0.53 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.013 0.001 TYR E 484 PHE 0.021 0.001 PHE E 233 TRP 0.019 0.002 TRP H 36 HIS 0.014 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (16905) covalent geometry : angle 0.63964 (22962) SS BOND : bond 0.00287 ( 34) SS BOND : angle 0.95470 ( 68) hydrogen bonds : bond 0.04059 ( 460) hydrogen bonds : angle 5.11725 ( 1200) Misc. bond : bond 0.00432 ( 2) link_ALPHA1-3 : bond 0.00893 ( 7) link_ALPHA1-3 : angle 2.31858 ( 21) link_ALPHA1-6 : bond 0.00566 ( 7) link_ALPHA1-6 : angle 1.80909 ( 21) link_BETA1-4 : bond 0.00701 ( 34) link_BETA1-4 : angle 2.32517 ( 102) link_NAG-ASN : bond 0.00533 ( 55) link_NAG-ASN : angle 3.14907 ( 165) *********************** 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 225 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.817 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: 0.8712 (m-10) cc_final: 0.8143 (m-10) REVERT: A 104 MET cc_start: 0.9272 (ttm) cc_final: 0.8993 (ttm) REVERT: A 180 ASP cc_start: 0.8745 (m-30) cc_final: 0.8096 (m-30) REVERT: A 374 HIS cc_start: 0.8184 (t70) cc_final: 0.7553 (t-90) REVERT: A 434 MET cc_start: 0.8847 (ptp) cc_final: 0.8420 (ptp) REVERT: C 53 PHE cc_start: 0.8458 (m-80) cc_final: 0.7954 (m-80) REVERT: C 69 TRP cc_start: 0.8857 (m-90) cc_final: 0.7741 (m-10) REVERT: C 111 LEU cc_start: 0.9411 (mm) cc_final: 0.9050 (mt) REVERT: C 116 LEU cc_start: 0.9395 (tt) cc_final: 0.9034 (mp) REVERT: C 210 PHE cc_start: 0.8981 (m-80) cc_final: 0.8506 (m-10) REVERT: C 260 LEU cc_start: 0.9292 (mt) cc_final: 0.8983 (mt) REVERT: D 584 GLU cc_start: 0.9231 (tp30) cc_final: 0.8316 (tm-30) REVERT: D 590 GLN cc_start: 0.9334 (tp40) cc_final: 0.8955 (tp40) REVERT: E 92 GLU cc_start: 0.8732 (tt0) cc_final: 0.8454 (tt0) REVERT: E 180 ASP cc_start: 0.8906 (m-30) cc_final: 0.8278 (m-30) REVERT: F 530 MET cc_start: 0.8417 (ptt) cc_final: 0.7746 (mtm) REVERT: F 576 LEU cc_start: 0.8562 (mt) cc_final: 0.7983 (tt) REVERT: F 584 GLU cc_start: 0.8498 (tp30) cc_final: 0.7942 (tm-30) REVERT: F 601 LYS cc_start: 0.8744 (tptt) cc_final: 0.8154 (tppp) REVERT: F 647 GLU cc_start: 0.8345 (pt0) cc_final: 0.7985 (pt0) REVERT: F 652 GLN cc_start: 0.8261 (tp40) cc_final: 0.7930 (tp-100) REVERT: B 540 GLN cc_start: 0.9160 (mm110) cc_final: 0.8061 (mt0) REVERT: B 601 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8547 (mmmm) REVERT: B 607 ASN cc_start: 0.8204 (m-40) cc_final: 0.7990 (m-40) REVERT: B 633 LYS cc_start: 0.9463 (mttt) cc_final: 0.9228 (mtmt) REVERT: L 49 TYR cc_start: 0.9226 (p90) cc_final: 0.8406 (p90) REVERT: L 53 ASN cc_start: 0.9042 (m-40) cc_final: 0.8540 (t0) REVERT: L 91 TYR cc_start: 0.7631 (t80) cc_final: 0.7372 (t80) REVERT: H 13 GLN cc_start: 0.8810 (mm110) cc_final: 0.8362 (mm-40) REVERT: H 68 THR cc_start: 0.8916 (m) cc_final: 0.8468 (p) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1225 time to fit residues: 43.2845 Evaluate side-chains 173 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 76 optimal weight: 0.0070 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 591 GLN B 575 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.049927 restraints weight = 69631.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051771 restraints weight = 40498.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053071 restraints weight = 28309.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053997 restraints weight = 22226.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054579 restraints weight = 18727.724| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4985 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= 0.141 Angle : 0.689 18.678 23339 Z= 0.325 Chirality : 0.048 0.415 2879 Planarity : 0.004 0.053 2788 Dihedral : 7.699 67.849 4217 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 1894 helix: 0.34 (0.26), residues: 411 sheet: 0.02 (0.22), residues: 566 loop : -0.54 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.012 0.001 TYR E 484 PHE 0.027 0.001 PHE E 233 TRP 0.020 0.002 TRP H 36 HIS 0.007 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00310 (16905) covalent geometry : angle 0.61896 (22962) SS BOND : bond 0.00308 ( 34) SS BOND : angle 0.90479 ( 68) hydrogen bonds : bond 0.03922 ( 460) hydrogen bonds : angle 5.09396 ( 1200) Misc. bond : bond 0.00467 ( 2) link_ALPHA1-3 : bond 0.00848 ( 7) link_ALPHA1-3 : angle 2.31146 ( 21) link_ALPHA1-6 : bond 0.00583 ( 7) link_ALPHA1-6 : angle 1.76236 ( 21) link_BETA1-4 : bond 0.00635 ( 34) link_BETA1-4 : angle 2.29538 ( 102) link_NAG-ASN : bond 0.00504 ( 55) link_NAG-ASN : angle 3.01659 ( 165) *********************** 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 221 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8724 (m-10) cc_final: 0.8169 (m-10) REVERT: A 104 MET cc_start: 0.9257 (ttm) cc_final: 0.8991 (ttm) REVERT: A 180 ASP cc_start: 0.8738 (m-30) cc_final: 0.8139 (m-30) REVERT: A 374 HIS cc_start: 0.8185 (t70) cc_final: 0.7271 (t70) REVERT: A 434 MET cc_start: 0.8949 (ptp) cc_final: 0.8613 (ptp) REVERT: C 53 PHE cc_start: 0.8380 (m-80) cc_final: 0.7593 (m-80) REVERT: C 69 TRP cc_start: 0.8876 (m-90) cc_final: 0.7755 (m-10) REVERT: C 111 LEU cc_start: 0.9387 (mm) cc_final: 0.9042 (mt) REVERT: C 116 LEU cc_start: 0.9396 (tt) cc_final: 0.9088 (mt) REVERT: C 210 PHE cc_start: 0.8856 (m-80) cc_final: 0.8458 (m-10) REVERT: C 260 LEU cc_start: 0.9219 (mt) cc_final: 0.8901 (mt) REVERT: D 584 GLU cc_start: 0.9246 (tp30) cc_final: 0.8381 (tm-30) REVERT: D 590 GLN cc_start: 0.9347 (tp40) cc_final: 0.8997 (tp40) REVERT: D 657 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8489 (mt-10) REVERT: E 92 GLU cc_start: 0.8723 (tt0) cc_final: 0.8522 (tt0) REVERT: E 95 MET cc_start: 0.8748 (mmm) cc_final: 0.8509 (mmm) REVERT: E 180 ASP cc_start: 0.8896 (m-30) cc_final: 0.8263 (m-30) REVERT: F 576 LEU cc_start: 0.8605 (mt) cc_final: 0.8021 (tt) REVERT: F 584 GLU cc_start: 0.8527 (tp30) cc_final: 0.7942 (tm-30) REVERT: F 647 GLU cc_start: 0.8347 (pt0) cc_final: 0.7929 (pt0) REVERT: F 652 GLN cc_start: 0.8294 (tp40) cc_final: 0.7970 (tp-100) REVERT: B 540 GLN cc_start: 0.9202 (mm110) cc_final: 0.8147 (mt0) REVERT: B 601 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8515 (mmmm) REVERT: L 49 TYR cc_start: 0.9229 (p90) cc_final: 0.8303 (p90) REVERT: L 53 ASN cc_start: 0.9060 (m-40) cc_final: 0.8561 (t0) REVERT: L 91 TYR cc_start: 0.7633 (t80) cc_final: 0.7370 (t80) REVERT: H 13 GLN cc_start: 0.8777 (mm110) cc_final: 0.8333 (mm-40) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1220 time to fit residues: 42.0540 Evaluate side-chains 172 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 172 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 HIS E 246 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN 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 = 0.3260 r_free = 0.3260 target = 0.066130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.049582 restraints weight = 70959.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051443 restraints weight = 41089.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052728 restraints weight = 28763.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.053654 restraints weight = 22653.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054282 restraints weight = 19183.615| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5172 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= 0.149 Angle : 0.693 18.540 23339 Z= 0.328 Chirality : 0.048 0.416 2879 Planarity : 0.004 0.055 2788 Dihedral : 7.510 68.671 4217 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 0.12 % Allowed : 1.00 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 1894 helix: 0.35 (0.27), residues: 408 sheet: -0.01 (0.22), residues: 568 loop : -0.54 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.010 0.001 TYR E 484 PHE 0.024 0.001 PHE E 233 TRP 0.020 0.002 TRP H 36 HIS 0.008 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00328 (16905) covalent geometry : angle 0.62690 (22962) SS BOND : bond 0.00312 ( 34) SS BOND : angle 0.90068 ( 68) hydrogen bonds : bond 0.03900 ( 460) hydrogen bonds : angle 5.15527 ( 1200) Misc. bond : bond 0.00401 ( 2) link_ALPHA1-3 : bond 0.00832 ( 7) link_ALPHA1-3 : angle 2.28548 ( 21) link_ALPHA1-6 : bond 0.00582 ( 7) link_ALPHA1-6 : angle 1.74498 ( 21) link_BETA1-4 : bond 0.00617 ( 34) link_BETA1-4 : angle 2.24780 ( 102) link_NAG-ASN : bond 0.00479 ( 55) link_NAG-ASN : angle 2.94001 ( 165) *********************** 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 215 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8737 (m-10) cc_final: 0.8128 (m-10) REVERT: A 104 MET cc_start: 0.9269 (ttm) cc_final: 0.8973 (ttm) REVERT: A 180 ASP cc_start: 0.8759 (m-30) cc_final: 0.8165 (m-30) REVERT: A 374 HIS cc_start: 0.8152 (t70) cc_final: 0.7244 (t70) REVERT: A 434 MET cc_start: 0.8985 (ptp) cc_final: 0.8633 (ptp) REVERT: C 53 PHE cc_start: 0.8221 (m-80) cc_final: 0.7697 (m-80) REVERT: C 111 LEU cc_start: 0.9385 (mm) cc_final: 0.9045 (mt) REVERT: C 210 PHE cc_start: 0.8896 (m-80) cc_final: 0.8598 (m-10) REVERT: C 260 LEU cc_start: 0.9215 (mt) cc_final: 0.8917 (mt) REVERT: D 584 GLU cc_start: 0.9189 (tp30) cc_final: 0.8344 (tm-30) REVERT: D 590 GLN cc_start: 0.9361 (tp40) cc_final: 0.8959 (tp40) REVERT: D 657 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 100 MET cc_start: 0.9241 (ttm) cc_final: 0.9040 (ttm) REVERT: E 180 ASP cc_start: 0.8915 (m-30) cc_final: 0.8270 (m-30) REVERT: F 576 LEU cc_start: 0.8599 (mt) cc_final: 0.8010 (tt) REVERT: F 584 GLU cc_start: 0.8551 (tp30) cc_final: 0.7961 (tm-30) REVERT: F 591 GLN cc_start: 0.9330 (tt0) cc_final: 0.8802 (tt0) REVERT: F 601 LYS cc_start: 0.8884 (tptt) cc_final: 0.8452 (tppp) REVERT: F 647 GLU cc_start: 0.8348 (pt0) cc_final: 0.7943 (pt0) REVERT: F 652 GLN cc_start: 0.8238 (tp40) cc_final: 0.7947 (tp-100) REVERT: B 540 GLN cc_start: 0.9150 (mm110) cc_final: 0.8118 (mt0) REVERT: B 591 GLN cc_start: 0.9258 (tp40) cc_final: 0.9037 (tp40) REVERT: B 601 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8521 (mmmm) REVERT: L 49 TYR cc_start: 0.9120 (p90) cc_final: 0.8329 (p90) REVERT: L 53 ASN cc_start: 0.9064 (m-40) cc_final: 0.8682 (t0) REVERT: H 13 GLN cc_start: 0.8813 (mm110) cc_final: 0.8376 (mm-40) REVERT: H 28 THR cc_start: 0.8771 (m) cc_final: 0.8496 (p) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.1238 time to fit residues: 41.6512 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 : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS E 85 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048732 restraints weight = 71814.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.050546 restraints weight = 42292.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051828 restraints weight = 29848.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052717 restraints weight = 23524.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053338 restraints weight = 19976.282| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17044 Z= 0.183 Angle : 0.726 18.272 23339 Z= 0.344 Chirality : 0.048 0.413 2879 Planarity : 0.004 0.059 2788 Dihedral : 7.490 68.166 4217 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1894 helix: 0.55 (0.28), residues: 381 sheet: -0.21 (0.22), residues: 568 loop : -0.54 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 66 TYR 0.017 0.002 TYR H 100R PHE 0.026 0.001 PHE E 233 TRP 0.027 0.002 TRP C 427 HIS 0.009 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00404 (16905) covalent geometry : angle 0.66083 (22962) SS BOND : bond 0.00361 ( 34) SS BOND : angle 0.93931 ( 68) hydrogen bonds : bond 0.04054 ( 460) hydrogen bonds : angle 5.15302 ( 1200) Misc. bond : bond 0.00377 ( 2) link_ALPHA1-3 : bond 0.00787 ( 7) link_ALPHA1-3 : angle 2.31845 ( 21) link_ALPHA1-6 : bond 0.00568 ( 7) link_ALPHA1-6 : angle 1.73796 ( 21) link_BETA1-4 : bond 0.00588 ( 34) link_BETA1-4 : angle 2.26266 ( 102) link_NAG-ASN : bond 0.00519 ( 55) link_NAG-ASN : angle 3.01628 ( 165) *********************** 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 206 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8787 (m-10) cc_final: 0.8230 (m-10) REVERT: A 180 ASP cc_start: 0.8773 (m-30) cc_final: 0.8518 (m-30) REVERT: A 374 HIS cc_start: 0.8163 (t70) cc_final: 0.7248 (t70) REVERT: A 434 MET cc_start: 0.9042 (ptp) cc_final: 0.8680 (ptp) REVERT: C 53 PHE cc_start: 0.8309 (m-80) cc_final: 0.7999 (m-10) REVERT: C 104 MET cc_start: 0.9024 (tmm) cc_final: 0.8720 (tmm) REVERT: C 111 LEU cc_start: 0.9433 (mm) cc_final: 0.9065 (mt) REVERT: C 210 PHE cc_start: 0.8959 (m-80) cc_final: 0.8609 (m-10) REVERT: C 260 LEU cc_start: 0.9266 (mt) cc_final: 0.8963 (mt) REVERT: D 584 GLU cc_start: 0.9206 (tp30) cc_final: 0.8379 (tm-30) REVERT: D 590 GLN cc_start: 0.9366 (tp40) cc_final: 0.9005 (tp40) REVERT: D 657 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8208 (mt-10) REVERT: E 180 ASP cc_start: 0.8953 (m-30) cc_final: 0.8207 (m-30) REVERT: F 576 LEU cc_start: 0.8617 (mt) cc_final: 0.8021 (tt) REVERT: F 584 GLU cc_start: 0.8513 (tp30) cc_final: 0.7986 (tm-30) REVERT: F 591 GLN cc_start: 0.9403 (tt0) cc_final: 0.8867 (tt0) REVERT: F 647 GLU cc_start: 0.8372 (pt0) cc_final: 0.7999 (pt0) REVERT: F 652 GLN cc_start: 0.8275 (tp40) cc_final: 0.7988 (tp-100) REVERT: B 540 GLN cc_start: 0.9180 (mm110) cc_final: 0.8053 (mt0) REVERT: B 601 LYS cc_start: 0.8999 (mmtp) cc_final: 0.8533 (mmmm) REVERT: L 49 TYR cc_start: 0.9111 (p90) cc_final: 0.8193 (p90) REVERT: L 53 ASN cc_start: 0.8993 (m-40) cc_final: 0.8587 (t0) REVERT: L 75 ILE cc_start: 0.8507 (mt) cc_final: 0.8177 (tt) REVERT: L 82 ASP cc_start: 0.6417 (m-30) cc_final: 0.5442 (m-30) REVERT: L 98 PHE cc_start: 0.7805 (m-80) cc_final: 0.7604 (m-10) REVERT: H 13 GLN cc_start: 0.8907 (mm110) cc_final: 0.8491 (mm-40) REVERT: H 20 LEU cc_start: 0.8809 (tp) cc_final: 0.8385 (tp) REVERT: H 28 THR cc_start: 0.8721 (m) cc_final: 0.8502 (p) REVERT: H 66 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.6273 (ptm-80) REVERT: H 67 PHE cc_start: 0.7868 (m-10) cc_final: 0.7569 (m-10) REVERT: H 83 ARG cc_start: 0.6762 (mtm110) cc_final: 0.6242 (mtm180) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1174 time to fit residues: 37.7393 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN E 85 HIS E 348 GLN E 478 ASN B 585 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.062522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.046026 restraints weight = 73788.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047722 restraints weight = 44230.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048910 restraints weight = 31572.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049736 restraints weight = 25072.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.050308 restraints weight = 21487.408| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17044 Z= 0.323 Angle : 0.908 18.007 23339 Z= 0.435 Chirality : 0.051 0.404 2879 Planarity : 0.005 0.054 2788 Dihedral : 8.233 70.970 4217 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1894 helix: -0.06 (0.26), residues: 390 sheet: -0.49 (0.22), residues: 538 loop : -0.92 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 66 TYR 0.025 0.002 TYR E 384 PHE 0.034 0.003 PHE E 53 TRP 0.039 0.004 TRP C 427 HIS 0.013 0.002 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00710 (16905) covalent geometry : angle 0.84828 (22962) SS BOND : bond 0.00544 ( 34) SS BOND : angle 1.29649 ( 68) hydrogen bonds : bond 0.04842 ( 460) hydrogen bonds : angle 5.68893 ( 1200) Misc. bond : bond 0.00343 ( 2) link_ALPHA1-3 : bond 0.00751 ( 7) link_ALPHA1-3 : angle 2.54619 ( 21) link_ALPHA1-6 : bond 0.00512 ( 7) link_ALPHA1-6 : angle 1.83970 ( 21) link_BETA1-4 : bond 0.00620 ( 34) link_BETA1-4 : angle 2.50272 ( 102) link_NAG-ASN : bond 0.00698 ( 55) link_NAG-ASN : angle 3.26489 ( 165) ********************** 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 180 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8716 (m-10) cc_final: 0.8272 (m-10) REVERT: A 104 MET cc_start: 0.9333 (ttm) cc_final: 0.9031 (ttm) REVERT: A 374 HIS cc_start: 0.8165 (t70) cc_final: 0.7307 (t70) REVERT: C 53 PHE cc_start: 0.8309 (m-80) cc_final: 0.7942 (m-10) REVERT: C 104 MET cc_start: 0.9221 (tmm) cc_final: 0.8865 (tmm) REVERT: C 207 LYS cc_start: 0.8590 (pttt) cc_final: 0.8291 (tptt) REVERT: D 584 GLU cc_start: 0.9250 (tp30) cc_final: 0.8366 (tm-30) REVERT: D 657 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8381 (mt-10) REVERT: E 180 ASP cc_start: 0.8961 (m-30) cc_final: 0.8242 (m-30) REVERT: E 479 TRP cc_start: 0.8976 (m-90) cc_final: 0.8031 (m-90) REVERT: F 576 LEU cc_start: 0.8731 (mt) cc_final: 0.8192 (tt) REVERT: F 584 GLU cc_start: 0.8656 (tp30) cc_final: 0.8182 (tm-30) REVERT: F 591 GLN cc_start: 0.9576 (tt0) cc_final: 0.9052 (tt0) REVERT: F 601 LYS cc_start: 0.8971 (tptt) cc_final: 0.8556 (tppt) REVERT: F 647 GLU cc_start: 0.8463 (pt0) cc_final: 0.8127 (pt0) REVERT: B 601 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8585 (mmmm) REVERT: L 49 TYR cc_start: 0.9130 (p90) cc_final: 0.8075 (p90) REVERT: L 53 ASN cc_start: 0.8934 (m-40) cc_final: 0.8566 (t0) REVERT: L 91 TYR cc_start: 0.7349 (t80) cc_final: 0.6932 (t80) REVERT: H 13 GLN cc_start: 0.8968 (mm110) cc_final: 0.8577 (mm-40) REVERT: H 20 LEU cc_start: 0.8675 (tp) cc_final: 0.8283 (tp) REVERT: H 67 PHE cc_start: 0.7885 (m-10) cc_final: 0.7676 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1248 time to fit residues: 34.4007 Evaluate side-chains 135 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 HIS ** 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 = 0.3253 r_free = 0.3253 target = 0.065839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049430 restraints weight = 70277.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051278 restraints weight = 40995.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052550 restraints weight = 28586.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053465 restraints weight = 22476.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054089 restraints weight = 18969.678| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17044 Z= 0.130 Angle : 0.707 18.623 23339 Z= 0.338 Chirality : 0.049 0.388 2879 Planarity : 0.004 0.052 2788 Dihedral : 7.545 70.793 4217 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1894 helix: 0.22 (0.27), residues: 396 sheet: -0.33 (0.23), residues: 521 loop : -0.73 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 66 TYR 0.015 0.001 TYR E 484 PHE 0.025 0.001 PHE E 233 TRP 0.025 0.002 TRP E 479 HIS 0.013 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00280 (16905) covalent geometry : angle 0.64807 (22962) SS BOND : bond 0.00319 ( 34) SS BOND : angle 0.84669 ( 68) hydrogen bonds : bond 0.04087 ( 460) hydrogen bonds : angle 5.18590 ( 1200) Misc. bond : bond 0.00571 ( 2) link_ALPHA1-3 : bond 0.00872 ( 7) link_ALPHA1-3 : angle 2.12565 ( 21) link_ALPHA1-6 : bond 0.00610 ( 7) link_ALPHA1-6 : angle 1.67280 ( 21) link_BETA1-4 : bond 0.00657 ( 34) link_BETA1-4 : angle 2.11473 ( 102) link_NAG-ASN : bond 0.00530 ( 55) link_NAG-ASN : angle 2.88055 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.93 seconds wall clock time: 43 minutes 46.34 seconds (2626.34 seconds total)