Starting phenix.real_space_refine on Sun Aug 24 05:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.map" model { file = "/net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t77_25736/08_2025/7t77_25736.cif" } resolution = 4.75 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= 0.010 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10473 2.51 5 N 2801 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1077 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.40, per 1000 atoms: 0.26 Number of scatterers: 16832 At special positions: 0 Unit cell: (129.95, 125.35, 165.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3453 8.00 N 2801 7.00 C 10473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.14 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.08 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.16 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA h 3 " - " MAN h 7 " " MAN h 4 " - " MAN h 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 6 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 130 " " NAG A 607 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 185h" " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 448 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 130 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 301 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 448 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN E 130 " " NAG j 1 " - " ASN E 156 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 749.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 25 sheets defined 24.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.516A pdb=" N LYS B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.588A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.175A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.733A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.760A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 460 through 464 removed outlier: 4.273A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.740A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.528A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100I through 100M Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.502A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.595A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.758A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 3.745A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AB5, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AB6, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 removed outlier: 5.520A pdb=" N ILE E 215 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY E 250 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR E 217 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'E' and resid 201 through 202 removed outlier: 7.890A pdb=" N GLN E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET E 426 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 302 removed outlier: 7.792A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.812A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 49 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 19 through 24 480 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 3357 1.32 - 1.47: 6058 1.47 - 1.61: 7591 1.61 - 1.76: 23 1.76 - 1.91: 127 Bond restraints: 17156 Sorted by residual: bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB LEU L 106A" pdb=" CG LEU L 106A" ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NE ARG H 3 " pdb=" CZ ARG H 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.33: 23251 7.33 - 14.65: 41 14.65 - 21.98: 1 21.98 - 29.31: 0 29.31 - 36.63: 3 Bond angle restraints: 23296 Sorted by residual: angle pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " pdb=" C7 NAG A 601 " ideal model delta sigma weight residual 124.56 161.19 -36.63 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C2 NAG E 605 " pdb=" N2 NAG E 605 " pdb=" C7 NAG E 605 " ideal model delta sigma weight residual 124.56 160.59 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 159.61 -35.05 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C HIS E 72 " pdb=" N ALA E 73 " pdb=" CA ALA E 73 " ideal model delta sigma weight residual 122.84 109.29 13.55 1.30e+00 5.92e-01 1.09e+02 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.85 128.36 -8.51 1.01e+00 9.80e-01 7.10e+01 ... (remaining 23291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 11169 21.61 - 43.21: 278 43.21 - 64.82: 86 64.82 - 86.43: 71 86.43 - 108.04: 33 Dihedral angle restraints: 11637 sinusoidal: 5999 harmonic: 5638 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 149.44 -56.44 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 11634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1855 0.107 - 0.214: 642 0.214 - 0.321: 242 0.321 - 0.428: 112 0.428 - 0.535: 62 Chirality restraints: 2913 Sorted by residual: chirality pdb=" C1 MAN R 5 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.36e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.68e+02 ... (remaining 2910 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG i 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG j 2 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.526 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG j 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.210 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4261 2.82 - 3.34: 15821 3.34 - 3.86: 28471 3.86 - 4.38: 34188 4.38 - 4.90: 51974 Nonbonded interactions: 134715 Sorted by model distance: nonbonded pdb=" O TRP E 69 " pdb=" N THR E 71 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS F 574 " model vdw 2.388 3.120 nonbonded pdb=" N GLY A 41 " pdb=" N VAL A 42 " model vdw 2.415 2.560 nonbonded pdb=" N LYS E 97 " pdb=" N ASN E 98 " model vdw 2.418 2.560 nonbonded pdb=" N ASP C 141 " pdb=" OD1 ASP C 141 " model vdw 2.441 3.120 ... (remaining 134710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 32 through 607) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'i' } ncs_group { reference = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'j' and (resid 1 or resid 4 through 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.630 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.136 17295 Z= 1.195 Angle : 1.868 36.634 23679 Z= 1.162 Chirality : 0.153 0.535 2913 Planarity : 0.016 0.304 2833 Dihedral : 13.668 108.037 7897 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.71 % Favored : 97.03 % Rotamer: Outliers : 0.87 % Allowed : 0.93 % Favored : 98.20 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.19), residues: 1918 helix: -0.47 (0.23), residues: 417 sheet: 0.70 (0.21), residues: 558 loop : 0.50 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 350 TYR 0.054 0.008 TYR C 40 PHE 0.045 0.007 PHE C 93 TRP 0.054 0.008 TRP E 479 HIS 0.010 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.02187 (17156) covalent geometry : angle 1.82781 (23296) SS BOND : bond 0.03725 ( 34) SS BOND : angle 3.00027 ( 68) hydrogen bonds : bond 0.15932 ( 480) hydrogen bonds : angle 7.88011 ( 1245) link_ALPHA1-3 : bond 0.03632 ( 5) link_ALPHA1-3 : angle 2.17157 ( 15) link_ALPHA1-6 : bond 0.03867 ( 4) link_ALPHA1-6 : angle 5.07501 ( 12) link_BETA1-4 : bond 0.06823 ( 36) link_BETA1-4 : angle 4.88253 ( 108) link_NAG-ASN : bond 0.07869 ( 60) link_NAG-ASN : angle 2.59678 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9519 (mt) cc_final: 0.9049 (tp) REVERT: A 180 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (m-30) REVERT: A 271 ILE cc_start: 0.9434 (mt) cc_final: 0.9209 (tp) REVERT: A 423 ILE cc_start: 0.9118 (mt) cc_final: 0.8755 (mm) REVERT: B 528 SER cc_start: 0.8591 (m) cc_final: 0.7830 (t) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8383 (mtm) REVERT: B 584 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8939 (tp30) REVERT: B 647 GLU cc_start: 0.8993 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 651 ASN cc_start: 0.8977 (m-40) cc_final: 0.8690 (p0) REVERT: B 654 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7934 (tm-30) REVERT: C 53 PHE cc_start: 0.7879 (m-80) cc_final: 0.7627 (m-10) REVERT: C 101 VAL cc_start: 0.9492 (t) cc_final: 0.9286 (p) REVERT: C 383 PHE cc_start: 0.9129 (m-80) cc_final: 0.8804 (m-80) REVERT: C 384 TYR cc_start: 0.8917 (m-80) cc_final: 0.8440 (m-80) REVERT: C 424 ILE cc_start: 0.8785 (mt) cc_final: 0.8583 (mm) REVERT: D 536 THR cc_start: 0.9269 (p) cc_final: 0.8962 (t) REVERT: D 538 THR cc_start: 0.9005 (p) cc_final: 0.7872 (p) REVERT: D 650 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7904 (tp40) REVERT: E 42 VAL cc_start: 0.9085 (t) cc_final: 0.8673 (t) REVERT: E 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8294 (m-90) REVERT: E 87 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8431 (t0) REVERT: E 254 VAL cc_start: 0.9475 (t) cc_final: 0.9233 (p) REVERT: F 530 MET cc_start: 0.9365 (mtp) cc_final: 0.9047 (mtp) REVERT: F 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8619 (tpp) REVERT: F 540 GLN cc_start: 0.8731 (mm110) cc_final: 0.8004 (mt0) REVERT: F 573 ILE cc_start: 0.8643 (mt) cc_final: 0.8334 (mm) REVERT: F 574 LYS cc_start: 0.8958 (mttt) cc_final: 0.8475 (mtmt) REVERT: F 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8871 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9346 (mmmt) REVERT: F 643 TYR cc_start: 0.9363 (m-10) cc_final: 0.9009 (m-80) REVERT: F 648 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8551 (tt0) REVERT: F 660 LEU cc_start: 0.8323 (mt) cc_final: 0.8029 (mt) REVERT: H 28 ASP cc_start: 0.8808 (t0) cc_final: 0.8297 (t0) REVERT: H 67 LEU cc_start: 0.8266 (mt) cc_final: 0.8016 (mm) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9046 (tp) REVERT: H 82 MET cc_start: 0.9002 (ptp) cc_final: 0.8520 (ttt) REVERT: H 91 PHE cc_start: 0.9263 (m-80) cc_final: 0.8933 (m-80) REVERT: L 4 LEU cc_start: 0.8996 (mt) cc_final: 0.8675 (tt) REVERT: L 36 TYR cc_start: 0.8280 (m-80) cc_final: 0.7911 (m-80) REVERT: L 69 ASN cc_start: 0.8219 (m-40) cc_final: 0.7683 (m-40) REVERT: L 78 LEU cc_start: 0.8730 (tp) cc_final: 0.8527 (tt) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7463 (m-30) REVERT: L 88 CYS cc_start: 0.3702 (p) cc_final: 0.3100 (p) REVERT: L 96 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8662 (mmt90) outliers start: 15 outliers final: 6 residues processed: 406 average time/residue: 0.1397 time to fit residues: 83.2955 Evaluate side-chains 207 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 652 GLN B 658 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 136 ASN E 195 ASN F 543 ASN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044786 restraints weight = 91824.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046643 restraints weight = 53691.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047995 restraints weight = 36661.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048943 restraints weight = 27612.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049654 restraints weight = 22385.528| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17295 Z= 0.172 Angle : 0.855 17.492 23679 Z= 0.407 Chirality : 0.050 0.374 2913 Planarity : 0.004 0.048 2833 Dihedral : 11.329 81.862 4264 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.35 % Allowed : 1.74 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1918 helix: 1.02 (0.26), residues: 372 sheet: 0.33 (0.21), residues: 582 loop : -0.05 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 192 TYR 0.038 0.002 TYR C 484 PHE 0.026 0.002 PHE A 233 TRP 0.030 0.002 TRP L 35 HIS 0.013 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00374 (17156) covalent geometry : angle 0.76982 (23296) SS BOND : bond 0.00431 ( 34) SS BOND : angle 1.30709 ( 68) hydrogen bonds : bond 0.05681 ( 480) hydrogen bonds : angle 6.32978 ( 1245) link_ALPHA1-3 : bond 0.00934 ( 5) link_ALPHA1-3 : angle 2.13153 ( 15) link_ALPHA1-6 : bond 0.02011 ( 4) link_ALPHA1-6 : angle 3.17242 ( 12) link_BETA1-4 : bond 0.00846 ( 36) link_BETA1-4 : angle 3.30795 ( 108) link_NAG-ASN : bond 0.00559 ( 60) link_NAG-ASN : angle 3.34030 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 265 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.9020 (m-30) cc_final: 0.8255 (m-30) REVERT: A 201 ILE cc_start: 0.9264 (mp) cc_final: 0.8457 (tp) REVERT: A 260 LEU cc_start: 0.9615 (mt) cc_final: 0.9326 (mp) REVERT: A 271 ILE cc_start: 0.9215 (mt) cc_final: 0.8975 (tp) REVERT: A 423 ILE cc_start: 0.9009 (mt) cc_final: 0.8581 (mm) REVERT: A 425 ASN cc_start: 0.8415 (p0) cc_final: 0.8032 (p0) REVERT: A 491 ILE cc_start: 0.9081 (tp) cc_final: 0.8704 (tp) REVERT: A 492 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8191 (mp0) REVERT: A 494 LEU cc_start: 0.8283 (mt) cc_final: 0.7774 (mt) REVERT: B 528 SER cc_start: 0.8485 (m) cc_final: 0.7770 (t) REVERT: B 574 LYS cc_start: 0.8969 (pptt) cc_final: 0.8739 (tmtt) REVERT: B 647 GLU cc_start: 0.9033 (tt0) cc_final: 0.8190 (mm-30) REVERT: B 648 GLU cc_start: 0.9119 (tp30) cc_final: 0.8886 (tp30) REVERT: B 654 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8107 (pt0) REVERT: C 98 ASN cc_start: 0.9150 (t0) cc_final: 0.8939 (m-40) REVERT: C 186 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7240 (ptm160) REVERT: C 217 TYR cc_start: 0.7413 (m-10) cc_final: 0.7155 (m-10) REVERT: C 489 VAL cc_start: 0.8941 (m) cc_final: 0.8715 (t) REVERT: D 536 THR cc_start: 0.8994 (p) cc_final: 0.8725 (t) REVERT: D 584 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8844 (tp30) REVERT: D 650 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7610 (tp-100) REVERT: E 69 TRP cc_start: 0.8637 (m-90) cc_final: 0.8116 (m-10) REVERT: E 98 ASN cc_start: 0.9179 (t0) cc_final: 0.7965 (t0) REVERT: E 434 MET cc_start: 0.8605 (mtp) cc_final: 0.8402 (mtp) REVERT: E 475 MET cc_start: 0.7509 (mtp) cc_final: 0.6922 (mtp) REVERT: F 535 MET cc_start: 0.8781 (mmp) cc_final: 0.8455 (tpp) REVERT: F 536 THR cc_start: 0.9199 (t) cc_final: 0.8964 (p) REVERT: F 633 LYS cc_start: 0.9694 (mttt) cc_final: 0.9297 (mmmt) REVERT: H 12 VAL cc_start: 0.8473 (m) cc_final: 0.8124 (m) REVERT: H 28 ASP cc_start: 0.8719 (t0) cc_final: 0.8429 (t70) REVERT: H 45 LEU cc_start: 0.9283 (mm) cc_final: 0.8913 (mm) REVERT: H 78 LEU cc_start: 0.9395 (tp) cc_final: 0.9099 (tp) REVERT: H 82 MET cc_start: 0.9039 (ptp) cc_final: 0.8830 (ttt) REVERT: H 82 ASN cc_start: 0.8193 (m-40) cc_final: 0.7916 (p0) REVERT: H 100 MET cc_start: 0.9225 (mpp) cc_final: 0.8854 (mpp) REVERT: L 36 TYR cc_start: 0.8271 (m-80) cc_final: 0.6739 (m-80) REVERT: L 50 ASP cc_start: 0.7987 (m-30) cc_final: 0.7351 (m-30) REVERT: L 69 ASN cc_start: 0.8338 (m-40) cc_final: 0.7659 (m-40) REVERT: L 86 TYR cc_start: 0.8566 (m-80) cc_final: 0.8001 (m-80) REVERT: L 89 LYS cc_start: 0.9254 (ttpp) cc_final: 0.8939 (ttpt) REVERT: L 92 THR cc_start: 0.8618 (p) cc_final: 0.8185 (t) REVERT: L 104 LEU cc_start: 0.8842 (tt) cc_final: 0.8429 (tt) outliers start: 6 outliers final: 3 residues processed: 270 average time/residue: 0.1143 time to fit residues: 48.7881 Evaluate side-chains 182 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 585 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 302 ASN D 585 HIS D 625 ASN D 651 ASN E 374 HIS L 1 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041974 restraints weight = 91939.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043799 restraints weight = 53028.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.045135 restraints weight = 35933.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.046057 restraints weight = 26941.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046785 restraints weight = 21837.888| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17295 Z= 0.179 Angle : 0.751 9.316 23679 Z= 0.359 Chirality : 0.047 0.300 2913 Planarity : 0.004 0.043 2833 Dihedral : 9.170 74.832 4264 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 0.16 (0.19), residues: 1918 helix: 0.91 (0.26), residues: 372 sheet: 0.19 (0.21), residues: 565 loop : -0.15 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 186 TYR 0.019 0.002 TYR D 643 PHE 0.018 0.002 PHE H 100J TRP 0.032 0.002 TRP D 596 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00386 (17156) covalent geometry : angle 0.68723 (23296) SS BOND : bond 0.00433 ( 34) SS BOND : angle 1.33104 ( 68) hydrogen bonds : bond 0.04567 ( 480) hydrogen bonds : angle 6.01892 ( 1245) link_ALPHA1-3 : bond 0.00881 ( 5) link_ALPHA1-3 : angle 1.92819 ( 15) link_ALPHA1-6 : bond 0.01644 ( 4) link_ALPHA1-6 : angle 2.52833 ( 12) link_BETA1-4 : bond 0.00647 ( 36) link_BETA1-4 : angle 2.74643 ( 108) link_NAG-ASN : bond 0.00437 ( 60) link_NAG-ASN : angle 2.68765 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.529 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: A 98 ASN cc_start: 0.9414 (t0) cc_final: 0.9002 (t0) REVERT: A 180 ASP cc_start: 0.9032 (m-30) cc_final: 0.8183 (m-30) REVERT: A 201 ILE cc_start: 0.9388 (mp) cc_final: 0.8623 (tp) REVERT: A 271 ILE cc_start: 0.9359 (mt) cc_final: 0.9112 (tp) REVERT: A 423 ILE cc_start: 0.9013 (mt) cc_final: 0.8635 (mm) REVERT: A 425 ASN cc_start: 0.8428 (p0) cc_final: 0.8090 (p0) REVERT: A 434 MET cc_start: 0.8684 (tpp) cc_final: 0.8397 (tpp) REVERT: A 491 ILE cc_start: 0.8923 (tp) cc_final: 0.8692 (tp) REVERT: A 492 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8382 (mp0) REVERT: A 494 LEU cc_start: 0.8587 (mt) cc_final: 0.8049 (mt) REVERT: B 626 MET cc_start: 0.8519 (mmp) cc_final: 0.7951 (mmm) REVERT: B 647 GLU cc_start: 0.9434 (tt0) cc_final: 0.9141 (tm-30) REVERT: B 651 ASN cc_start: 0.9111 (p0) cc_final: 0.8886 (p0) REVERT: B 654 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8156 (pt0) REVERT: C 150 MET cc_start: 0.8874 (mmp) cc_final: 0.8452 (mmm) REVERT: C 186 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7224 (ptm160) REVERT: D 536 THR cc_start: 0.8943 (p) cc_final: 0.8733 (t) REVERT: D 584 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8894 (tp30) REVERT: D 595 ILE cc_start: 0.9424 (tt) cc_final: 0.9041 (tt) REVERT: D 626 MET cc_start: 0.9090 (tpp) cc_final: 0.8865 (tpp) REVERT: E 67 ASN cc_start: 0.9000 (m-40) cc_final: 0.8799 (t0) REVERT: E 69 TRP cc_start: 0.8614 (m-90) cc_final: 0.8169 (m-90) REVERT: E 98 ASN cc_start: 0.9220 (t0) cc_final: 0.7792 (t0) REVERT: E 434 MET cc_start: 0.8913 (mtm) cc_final: 0.8357 (mtm) REVERT: E 483 LEU cc_start: 0.8723 (mt) cc_final: 0.7885 (mt) REVERT: F 535 MET cc_start: 0.8799 (mmp) cc_final: 0.8475 (tpp) REVERT: F 601 LYS cc_start: 0.9025 (mttt) cc_final: 0.8201 (mtmt) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9294 (mmmt) REVERT: H 28 ASP cc_start: 0.8823 (t0) cc_final: 0.8534 (t70) REVERT: H 45 LEU cc_start: 0.9416 (mm) cc_final: 0.9043 (mm) REVERT: H 78 LEU cc_start: 0.9493 (tp) cc_final: 0.9222 (tp) REVERT: H 82 MET cc_start: 0.9209 (ptp) cc_final: 0.8992 (tpt) REVERT: L 35 TRP cc_start: 0.7623 (m100) cc_final: 0.7326 (m100) REVERT: L 86 TYR cc_start: 0.8689 (m-80) cc_final: 0.8009 (m-80) REVERT: L 88 CYS cc_start: 0.3545 (p) cc_final: 0.2925 (p) REVERT: L 104 LEU cc_start: 0.9076 (tt) cc_final: 0.8606 (tt) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.1025 time to fit residues: 35.0921 Evaluate side-chains 156 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN E 105 HIS F 570 HIS H 100RHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.041366 restraints weight = 95643.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043113 restraints weight = 56179.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.044406 restraints weight = 38761.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045313 restraints weight = 29448.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045985 restraints weight = 24050.732| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17295 Z= 0.151 Angle : 0.684 10.876 23679 Z= 0.329 Chirality : 0.046 0.322 2913 Planarity : 0.004 0.102 2833 Dihedral : 7.674 69.577 4264 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.19), residues: 1918 helix: 0.89 (0.27), residues: 378 sheet: 0.07 (0.21), residues: 586 loop : -0.25 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 327 TYR 0.028 0.002 TYR F 586 PHE 0.020 0.002 PHE A 233 TRP 0.018 0.002 TRP L 35 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00325 (17156) covalent geometry : angle 0.62476 (23296) SS BOND : bond 0.00341 ( 34) SS BOND : angle 1.06983 ( 68) hydrogen bonds : bond 0.04097 ( 480) hydrogen bonds : angle 5.69739 ( 1245) link_ALPHA1-3 : bond 0.00941 ( 5) link_ALPHA1-3 : angle 1.76455 ( 15) link_ALPHA1-6 : bond 0.01670 ( 4) link_ALPHA1-6 : angle 2.66709 ( 12) link_BETA1-4 : bond 0.00579 ( 36) link_BETA1-4 : angle 2.51003 ( 108) link_NAG-ASN : bond 0.00378 ( 60) link_NAG-ASN : angle 2.45002 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.641 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: 0.9394 (t0) cc_final: 0.8925 (t0) REVERT: A 180 ASP cc_start: 0.8856 (m-30) cc_final: 0.7793 (m-30) REVERT: A 201 ILE cc_start: 0.9438 (mp) cc_final: 0.8681 (tp) REVERT: A 271 ILE cc_start: 0.9402 (mt) cc_final: 0.9150 (tp) REVERT: A 423 ILE cc_start: 0.9044 (mt) cc_final: 0.8736 (mm) REVERT: A 425 ASN cc_start: 0.8313 (p0) cc_final: 0.7947 (p0) REVERT: A 494 LEU cc_start: 0.8438 (mt) cc_final: 0.7867 (mt) REVERT: B 626 MET cc_start: 0.8160 (mmp) cc_final: 0.7740 (mmm) REVERT: B 647 GLU cc_start: 0.9445 (tt0) cc_final: 0.9163 (tm-30) REVERT: C 150 MET cc_start: 0.9010 (mmp) cc_final: 0.8631 (mmm) REVERT: C 186 ARG cc_start: 0.8184 (mmp80) cc_final: 0.7179 (ptm160) REVERT: D 584 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8953 (tp30) REVERT: E 69 TRP cc_start: 0.8621 (m-90) cc_final: 0.8168 (m-90) REVERT: E 100 MET cc_start: 0.9413 (ptm) cc_final: 0.9155 (ptm) REVERT: E 434 MET cc_start: 0.8919 (mtm) cc_final: 0.8507 (mtm) REVERT: E 478 ASN cc_start: 0.8879 (t0) cc_final: 0.8638 (t0) REVERT: F 570 HIS cc_start: 0.7061 (p-80) cc_final: 0.6407 (p90) REVERT: F 571 TRP cc_start: 0.7563 (m100) cc_final: 0.7201 (m100) REVERT: F 601 LYS cc_start: 0.9087 (mttt) cc_final: 0.8670 (mtmt) REVERT: F 633 LYS cc_start: 0.9649 (mttt) cc_final: 0.9301 (mmmt) REVERT: H 28 ASP cc_start: 0.8903 (t0) cc_final: 0.8448 (m-30) REVERT: H 45 LEU cc_start: 0.9394 (mm) cc_final: 0.8996 (mm) REVERT: H 78 LEU cc_start: 0.9462 (tp) cc_final: 0.9181 (tp) REVERT: H 82 LEU cc_start: 0.9458 (mt) cc_final: 0.8561 (mt) REVERT: L 35 TRP cc_start: 0.7947 (m100) cc_final: 0.7627 (m100) REVERT: L 86 TYR cc_start: 0.8650 (m-80) cc_final: 0.8385 (m-80) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.1058 time to fit residues: 33.1471 Evaluate side-chains 149 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040548 restraints weight = 96233.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.042225 restraints weight = 57315.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043453 restraints weight = 39972.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044331 restraints weight = 30729.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044983 restraints weight = 25225.236| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17295 Z= 0.163 Angle : 0.668 10.246 23679 Z= 0.324 Chirality : 0.045 0.303 2913 Planarity : 0.004 0.049 2833 Dihedral : 7.199 66.857 4264 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -0.02 (0.19), residues: 1918 helix: 0.86 (0.27), residues: 378 sheet: 0.08 (0.21), residues: 562 loop : -0.33 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 186 TYR 0.019 0.002 TYR B 638 PHE 0.012 0.002 PHE H 91 TRP 0.021 0.002 TRP D 596 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00353 (17156) covalent geometry : angle 0.61533 (23296) SS BOND : bond 0.00403 ( 34) SS BOND : angle 1.11498 ( 68) hydrogen bonds : bond 0.03992 ( 480) hydrogen bonds : angle 5.59266 ( 1245) link_ALPHA1-3 : bond 0.00869 ( 5) link_ALPHA1-3 : angle 1.91216 ( 15) link_ALPHA1-6 : bond 0.01510 ( 4) link_ALPHA1-6 : angle 2.46092 ( 12) link_BETA1-4 : bond 0.00519 ( 36) link_BETA1-4 : angle 2.33658 ( 108) link_NAG-ASN : bond 0.00394 ( 60) link_NAG-ASN : angle 2.30574 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.477 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 98 ASN cc_start: 0.9390 (t0) cc_final: 0.9038 (t0) REVERT: A 150 MET cc_start: 0.7567 (ptp) cc_final: 0.7300 (ptp) REVERT: A 180 ASP cc_start: 0.8803 (m-30) cc_final: 0.7857 (m-30) REVERT: A 201 ILE cc_start: 0.9439 (mp) cc_final: 0.8695 (tp) REVERT: A 271 ILE cc_start: 0.9460 (mt) cc_final: 0.9250 (tp) REVERT: A 425 ASN cc_start: 0.8180 (p0) cc_final: 0.7848 (p0) REVERT: A 494 LEU cc_start: 0.8633 (mt) cc_final: 0.7928 (mt) REVERT: B 528 SER cc_start: 0.8970 (m) cc_final: 0.8767 (m) REVERT: B 626 MET cc_start: 0.8593 (mmp) cc_final: 0.8112 (mmm) REVERT: B 633 LYS cc_start: 0.9585 (mtmm) cc_final: 0.9369 (mtmm) REVERT: B 647 GLU cc_start: 0.9408 (tt0) cc_final: 0.9167 (tm-30) REVERT: B 651 ASN cc_start: 0.9403 (p0) cc_final: 0.8905 (p0) REVERT: B 657 GLU cc_start: 0.9021 (mp0) cc_final: 0.8699 (mp0) REVERT: C 52 LEU cc_start: 0.9267 (mp) cc_final: 0.9040 (mp) REVERT: C 150 MET cc_start: 0.9066 (mmp) cc_final: 0.8712 (mmm) REVERT: C 186 ARG cc_start: 0.8190 (mmp80) cc_final: 0.7182 (ptm160) REVERT: D 584 GLU cc_start: 0.9237 (mt-10) cc_final: 0.9006 (tp30) REVERT: D 591 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9173 (mm-40) REVERT: D 595 ILE cc_start: 0.9392 (tt) cc_final: 0.8423 (tt) REVERT: D 626 MET cc_start: 0.9491 (mmp) cc_final: 0.9185 (tpp) REVERT: E 69 TRP cc_start: 0.8669 (m-90) cc_final: 0.8153 (m-90) REVERT: E 434 MET cc_start: 0.8930 (mtm) cc_final: 0.8433 (mtm) REVERT: E 453 ILE cc_start: 0.8476 (mm) cc_final: 0.8130 (tp) REVERT: F 601 LYS cc_start: 0.9298 (mttt) cc_final: 0.8874 (mtmt) REVERT: F 633 LYS cc_start: 0.9640 (mttt) cc_final: 0.9279 (mmmt) REVERT: F 650 GLN cc_start: 0.7253 (tp40) cc_final: 0.6541 (tp40) REVERT: H 28 ASP cc_start: 0.9023 (t0) cc_final: 0.8522 (m-30) REVERT: H 34 MET cc_start: 0.9573 (mmp) cc_final: 0.9131 (mmp) REVERT: H 45 LEU cc_start: 0.9500 (mm) cc_final: 0.9250 (mm) REVERT: H 67 LEU cc_start: 0.8671 (mm) cc_final: 0.8379 (mm) REVERT: H 75 LYS cc_start: 0.9396 (mtmt) cc_final: 0.9105 (mtmt) REVERT: H 78 LEU cc_start: 0.9500 (tp) cc_final: 0.9229 (tp) REVERT: H 82 LEU cc_start: 0.9475 (mt) cc_final: 0.9196 (mt) REVERT: L 35 TRP cc_start: 0.7644 (m100) cc_final: 0.7050 (m100) REVERT: L 86 TYR cc_start: 0.8556 (m-80) cc_final: 0.8113 (m-10) REVERT: L 88 CYS cc_start: 0.3188 (t) cc_final: 0.2684 (t) REVERT: L 104 LEU cc_start: 0.9136 (tt) cc_final: 0.8767 (tt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1117 time to fit residues: 32.7702 Evaluate side-chains 148 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 591 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN D 651 ASN F 570 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.038586 restraints weight = 98512.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.040190 restraints weight = 59160.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.041344 restraints weight = 41599.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.042134 restraints weight = 32281.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.042727 restraints weight = 26992.364| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17295 Z= 0.205 Angle : 0.715 9.908 23679 Z= 0.349 Chirality : 0.046 0.288 2913 Planarity : 0.004 0.059 2833 Dihedral : 7.234 62.665 4264 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 1918 helix: 0.40 (0.26), residues: 399 sheet: -0.19 (0.22), residues: 546 loop : -0.49 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 186 TYR 0.020 0.002 TYR B 638 PHE 0.013 0.002 PHE E 382 TRP 0.018 0.002 TRP L 35 HIS 0.007 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00436 (17156) covalent geometry : angle 0.67307 (23296) SS BOND : bond 0.00411 ( 34) SS BOND : angle 1.09448 ( 68) hydrogen bonds : bond 0.04087 ( 480) hydrogen bonds : angle 5.63596 ( 1245) link_ALPHA1-3 : bond 0.00746 ( 5) link_ALPHA1-3 : angle 2.07224 ( 15) link_ALPHA1-6 : bond 0.01337 ( 4) link_ALPHA1-6 : angle 1.73809 ( 12) link_BETA1-4 : bond 0.00445 ( 36) link_BETA1-4 : angle 2.30035 ( 108) link_NAG-ASN : bond 0.00405 ( 60) link_NAG-ASN : angle 2.10108 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 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: A 201 ILE cc_start: 0.9489 (mp) cc_final: 0.8866 (tp) REVERT: A 425 ASN cc_start: 0.8103 (p0) cc_final: 0.7655 (p0) REVERT: B 591 GLN cc_start: 0.9333 (tt0) cc_final: 0.9062 (tp40) REVERT: B 601 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8171 (mmmm) REVERT: B 626 MET cc_start: 0.8420 (mmp) cc_final: 0.8025 (mmm) REVERT: B 647 GLU cc_start: 0.9444 (tt0) cc_final: 0.9236 (tt0) REVERT: B 651 ASN cc_start: 0.8999 (p0) cc_final: 0.8695 (p0) REVERT: B 654 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8209 (pt0) REVERT: C 150 MET cc_start: 0.9144 (mmp) cc_final: 0.8722 (mmp) REVERT: C 186 ARG cc_start: 0.8224 (mmp80) cc_final: 0.7272 (ptm160) REVERT: D 610 TRP cc_start: 0.7123 (p90) cc_final: 0.6663 (p90) REVERT: D 626 MET cc_start: 0.9513 (mmp) cc_final: 0.9156 (tpp) REVERT: D 650 GLN cc_start: 0.8642 (tp-100) cc_final: 0.7860 (tp-100) REVERT: E 69 TRP cc_start: 0.8762 (m-90) cc_final: 0.8265 (m-90) REVERT: E 100 MET cc_start: 0.9542 (ptm) cc_final: 0.9087 (ptt) REVERT: E 279 ASN cc_start: 0.8757 (t0) cc_final: 0.8135 (t0) REVERT: E 434 MET cc_start: 0.8836 (mtm) cc_final: 0.8460 (mtm) REVERT: E 453 ILE cc_start: 0.8658 (mm) cc_final: 0.8320 (tp) REVERT: E 483 LEU cc_start: 0.9336 (mt) cc_final: 0.8839 (mt) REVERT: F 601 LYS cc_start: 0.9413 (mttt) cc_final: 0.8935 (mtmt) REVERT: F 633 LYS cc_start: 0.9655 (mttt) cc_final: 0.9288 (mmmt) REVERT: F 650 GLN cc_start: 0.7457 (tp40) cc_final: 0.6676 (tp40) REVERT: F 655 LYS cc_start: 0.9523 (ttmm) cc_final: 0.8947 (ttmm) REVERT: H 18 LEU cc_start: 0.8588 (tp) cc_final: 0.7753 (tp) REVERT: H 28 ASP cc_start: 0.9025 (t0) cc_final: 0.8446 (m-30) REVERT: H 32 GLN cc_start: 0.9024 (mp10) cc_final: 0.8771 (mp10) REVERT: H 45 LEU cc_start: 0.9538 (mm) cc_final: 0.9206 (mm) REVERT: H 75 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9191 (mtmt) REVERT: H 78 LEU cc_start: 0.9533 (tp) cc_final: 0.9295 (tp) REVERT: H 82 LEU cc_start: 0.9473 (mt) cc_final: 0.9240 (mm) REVERT: L 23 CYS cc_start: 0.3707 (p) cc_final: 0.2394 (p) REVERT: L 35 TRP cc_start: 0.7948 (m100) cc_final: 0.6745 (m100) REVERT: L 88 CYS cc_start: 0.3588 (t) cc_final: 0.3075 (t) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.1156 time to fit residues: 33.0787 Evaluate side-chains 131 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 651 ASN F 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039820 restraints weight = 96417.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.041485 restraints weight = 57240.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.042680 restraints weight = 39918.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043509 restraints weight = 30795.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.044159 restraints weight = 25620.668| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17295 Z= 0.123 Angle : 0.634 11.971 23679 Z= 0.309 Chirality : 0.046 0.320 2913 Planarity : 0.004 0.051 2833 Dihedral : 6.896 59.691 4264 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.26 (0.19), residues: 1918 helix: 0.60 (0.27), residues: 393 sheet: -0.11 (0.22), residues: 546 loop : -0.44 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 186 TYR 0.016 0.001 TYR F 586 PHE 0.014 0.001 PHE L 62 TRP 0.037 0.002 TRP A 69 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00264 (17156) covalent geometry : angle 0.58537 (23296) SS BOND : bond 0.00329 ( 34) SS BOND : angle 0.82729 ( 68) hydrogen bonds : bond 0.03791 ( 480) hydrogen bonds : angle 5.39171 ( 1245) link_ALPHA1-3 : bond 0.00876 ( 5) link_ALPHA1-3 : angle 2.05991 ( 15) link_ALPHA1-6 : bond 0.01323 ( 4) link_ALPHA1-6 : angle 1.60420 ( 12) link_BETA1-4 : bond 0.00555 ( 36) link_BETA1-4 : angle 2.13521 ( 108) link_NAG-ASN : bond 0.00410 ( 60) link_NAG-ASN : angle 2.24535 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.468 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 150 MET cc_start: 0.8421 (ptp) cc_final: 0.8179 (ptt) REVERT: A 201 ILE cc_start: 0.9444 (mp) cc_final: 0.8897 (tp) REVERT: A 425 ASN cc_start: 0.8016 (p0) cc_final: 0.7621 (p0) REVERT: A 434 MET cc_start: 0.8637 (tpp) cc_final: 0.8356 (tpp) REVERT: A 491 ILE cc_start: 0.8917 (tp) cc_final: 0.8664 (tp) REVERT: A 494 LEU cc_start: 0.8742 (mt) cc_final: 0.8075 (mt) REVERT: B 528 SER cc_start: 0.9173 (m) cc_final: 0.8338 (p) REVERT: B 601 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7492 (mtmm) REVERT: B 626 MET cc_start: 0.8435 (mmp) cc_final: 0.7967 (mmm) REVERT: B 647 GLU cc_start: 0.9406 (tt0) cc_final: 0.9186 (tm-30) REVERT: B 654 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8026 (pt0) REVERT: B 657 GLU cc_start: 0.9016 (mp0) cc_final: 0.8559 (mp0) REVERT: B 658 GLN cc_start: 0.8906 (mp10) cc_final: 0.8621 (mp10) REVERT: C 150 MET cc_start: 0.9164 (mmp) cc_final: 0.8742 (mmp) REVERT: C 186 ARG cc_start: 0.8206 (mmp80) cc_final: 0.7294 (ptm160) REVERT: D 584 GLU cc_start: 0.9262 (tp30) cc_final: 0.8767 (tp30) REVERT: D 610 TRP cc_start: 0.7254 (p90) cc_final: 0.6866 (p90) REVERT: D 626 MET cc_start: 0.9505 (mmp) cc_final: 0.9197 (tpp) REVERT: D 650 GLN cc_start: 0.8587 (tp-100) cc_final: 0.7808 (tp-100) REVERT: E 69 TRP cc_start: 0.8693 (m-90) cc_final: 0.8179 (m-90) REVERT: E 100 MET cc_start: 0.9489 (ptm) cc_final: 0.8912 (ppp) REVERT: E 279 ASN cc_start: 0.8701 (t0) cc_final: 0.8077 (t0) REVERT: E 434 MET cc_start: 0.8888 (mtm) cc_final: 0.8563 (mtt) REVERT: E 453 ILE cc_start: 0.8534 (mm) cc_final: 0.8191 (tp) REVERT: E 478 ASN cc_start: 0.9051 (t0) cc_final: 0.8463 (t0) REVERT: E 479 TRP cc_start: 0.9008 (m-90) cc_final: 0.8289 (m-90) REVERT: F 545 LEU cc_start: 0.9016 (tp) cc_final: 0.8756 (tp) REVERT: F 601 LYS cc_start: 0.9308 (mttt) cc_final: 0.8790 (mtmt) REVERT: F 626 MET cc_start: 0.6988 (mpp) cc_final: 0.6468 (mpp) REVERT: F 633 LYS cc_start: 0.9629 (mttt) cc_final: 0.9261 (mmmt) REVERT: F 650 GLN cc_start: 0.7362 (tp40) cc_final: 0.6564 (tp40) REVERT: F 655 LYS cc_start: 0.9511 (ttmm) cc_final: 0.9009 (ttmm) REVERT: H 34 MET cc_start: 0.9548 (mmp) cc_final: 0.9215 (mmm) REVERT: H 45 LEU cc_start: 0.9512 (mm) cc_final: 0.9239 (mm) REVERT: L 23 CYS cc_start: 0.4291 (p) cc_final: 0.2698 (p) REVERT: L 35 TRP cc_start: 0.7935 (m100) cc_final: 0.6918 (m100) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1138 time to fit residues: 33.6246 Evaluate side-chains 139 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 0.0020 chunk 99 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 168 optimal weight: 30.0000 chunk 164 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN F 570 HIS F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.036947 restraints weight = 97582.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.038493 restraints weight = 58436.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.039603 restraints weight = 40899.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.040390 restraints weight = 31724.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.040962 restraints weight = 26388.412| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17295 Z= 0.252 Angle : 0.776 10.108 23679 Z= 0.377 Chirality : 0.047 0.283 2913 Planarity : 0.005 0.054 2833 Dihedral : 7.291 58.611 4264 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -0.66 (0.19), residues: 1918 helix: 0.16 (0.26), residues: 402 sheet: -0.35 (0.22), residues: 524 loop : -0.65 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 186 TYR 0.020 0.002 TYR E 217 PHE 0.017 0.003 PHE H 100J TRP 0.035 0.002 TRP A 69 HIS 0.008 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00538 (17156) covalent geometry : angle 0.73263 (23296) SS BOND : bond 0.00440 ( 34) SS BOND : angle 1.17054 ( 68) hydrogen bonds : bond 0.04370 ( 480) hydrogen bonds : angle 5.78429 ( 1245) link_ALPHA1-3 : bond 0.00591 ( 5) link_ALPHA1-3 : angle 2.36075 ( 15) link_ALPHA1-6 : bond 0.01077 ( 4) link_ALPHA1-6 : angle 1.68691 ( 12) link_BETA1-4 : bond 0.00504 ( 36) link_BETA1-4 : angle 2.34213 ( 108) link_NAG-ASN : bond 0.00525 ( 60) link_NAG-ASN : angle 2.31076 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8570 (ptp) cc_final: 0.8231 (ptt) REVERT: A 201 ILE cc_start: 0.9447 (mp) cc_final: 0.8965 (tp) REVERT: A 425 ASN cc_start: 0.8071 (p0) cc_final: 0.7536 (p0) REVERT: B 528 SER cc_start: 0.9299 (m) cc_final: 0.8671 (p) REVERT: B 536 THR cc_start: 0.9054 (m) cc_final: 0.8844 (p) REVERT: B 601 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8192 (mmmm) REVERT: B 626 MET cc_start: 0.8370 (mmp) cc_final: 0.8083 (mmm) REVERT: B 654 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8257 (pt0) REVERT: B 655 LYS cc_start: 0.9321 (pttp) cc_final: 0.9116 (pptt) REVERT: C 100 MET cc_start: 0.8623 (mmm) cc_final: 0.8313 (tpt) REVERT: C 104 MET cc_start: 0.9012 (ttm) cc_final: 0.8692 (ttt) REVERT: C 150 MET cc_start: 0.9257 (mmp) cc_final: 0.8898 (mmp) REVERT: C 434 MET cc_start: 0.7731 (ppp) cc_final: 0.7495 (ppp) REVERT: D 584 GLU cc_start: 0.9310 (tp30) cc_final: 0.8984 (tp30) REVERT: D 595 ILE cc_start: 0.9638 (tp) cc_final: 0.8804 (tp) REVERT: D 610 TRP cc_start: 0.7661 (p90) cc_final: 0.7288 (p90) REVERT: D 626 MET cc_start: 0.9498 (mmp) cc_final: 0.9234 (tpp) REVERT: D 650 GLN cc_start: 0.8761 (tp-100) cc_final: 0.7967 (tp-100) REVERT: D 651 ASN cc_start: 0.9596 (t160) cc_final: 0.9389 (t0) REVERT: E 69 TRP cc_start: 0.8818 (m-90) cc_final: 0.8346 (m-90) REVERT: E 100 MET cc_start: 0.9586 (ptm) cc_final: 0.9134 (ppp) REVERT: E 279 ASN cc_start: 0.8822 (t0) cc_final: 0.8179 (t0) REVERT: E 453 ILE cc_start: 0.8773 (mm) cc_final: 0.8467 (tp) REVERT: F 545 LEU cc_start: 0.9206 (tp) cc_final: 0.8809 (tp) REVERT: F 633 LYS cc_start: 0.9642 (mttt) cc_final: 0.9316 (mmmt) REVERT: F 650 GLN cc_start: 0.7621 (tp40) cc_final: 0.6755 (tp40) REVERT: F 655 LYS cc_start: 0.9535 (ttmm) cc_final: 0.8911 (ttmm) REVERT: H 18 LEU cc_start: 0.8695 (tp) cc_final: 0.7920 (tp) REVERT: H 32 GLN cc_start: 0.8962 (mp10) cc_final: 0.8629 (mp10) REVERT: H 34 MET cc_start: 0.9654 (mmp) cc_final: 0.9286 (mmm) REVERT: H 45 LEU cc_start: 0.9676 (mm) cc_final: 0.9445 (mm) REVERT: H 78 LEU cc_start: 0.9472 (tp) cc_final: 0.9202 (tp) REVERT: L 23 CYS cc_start: 0.4460 (p) cc_final: 0.2999 (p) REVERT: L 35 TRP cc_start: 0.8110 (m100) cc_final: 0.6877 (m100) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1091 time to fit residues: 28.1222 Evaluate side-chains 125 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN D 651 ASN F 570 HIS F 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.049817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.037841 restraints weight = 100104.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.039365 restraints weight = 60330.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040466 restraints weight = 42585.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.041251 restraints weight = 33316.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041817 restraints weight = 27887.180| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17295 Z= 0.176 Angle : 0.670 9.734 23679 Z= 0.329 Chirality : 0.046 0.264 2913 Planarity : 0.004 0.065 2833 Dihedral : 7.102 57.848 4264 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.19), residues: 1918 helix: 0.34 (0.26), residues: 396 sheet: -0.41 (0.22), residues: 527 loop : -0.66 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 186 TYR 0.022 0.002 TYR L 36 PHE 0.015 0.002 PHE E 382 TRP 0.042 0.002 TRP A 69 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00378 (17156) covalent geometry : angle 0.62780 (23296) SS BOND : bond 0.00343 ( 34) SS BOND : angle 1.02345 ( 68) hydrogen bonds : bond 0.03897 ( 480) hydrogen bonds : angle 5.48967 ( 1245) link_ALPHA1-3 : bond 0.00663 ( 5) link_ALPHA1-3 : angle 2.36391 ( 15) link_ALPHA1-6 : bond 0.01104 ( 4) link_ALPHA1-6 : angle 1.40842 ( 12) link_BETA1-4 : bond 0.00499 ( 36) link_BETA1-4 : angle 2.13357 ( 108) link_NAG-ASN : bond 0.00345 ( 60) link_NAG-ASN : angle 2.07344 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8577 (ptp) cc_final: 0.8331 (ptt) REVERT: A 201 ILE cc_start: 0.9382 (mp) cc_final: 0.8944 (tp) REVERT: A 425 ASN cc_start: 0.7972 (p0) cc_final: 0.7510 (p0) REVERT: A 494 LEU cc_start: 0.8866 (mt) cc_final: 0.8095 (mt) REVERT: B 528 SER cc_start: 0.9262 (m) cc_final: 0.8673 (p) REVERT: B 536 THR cc_start: 0.8980 (m) cc_final: 0.8779 (p) REVERT: B 601 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7458 (mtmm) REVERT: B 626 MET cc_start: 0.8296 (mmp) cc_final: 0.7984 (mmm) REVERT: B 633 LYS cc_start: 0.9722 (mtpt) cc_final: 0.9341 (mtmm) REVERT: B 655 LYS cc_start: 0.9288 (pttp) cc_final: 0.8981 (pptt) REVERT: B 658 GLN cc_start: 0.9123 (mp10) cc_final: 0.8905 (mp10) REVERT: C 100 MET cc_start: 0.8462 (mmm) cc_final: 0.8192 (tpt) REVERT: C 104 MET cc_start: 0.8975 (ttm) cc_final: 0.8605 (ttt) REVERT: C 150 MET cc_start: 0.9269 (mmp) cc_final: 0.8923 (mmp) REVERT: C 434 MET cc_start: 0.7687 (ppp) cc_final: 0.7471 (ppp) REVERT: C 475 MET cc_start: 0.8759 (mmp) cc_final: 0.8195 (mmp) REVERT: D 535 MET cc_start: 0.9045 (mmp) cc_final: 0.8819 (mmm) REVERT: D 584 GLU cc_start: 0.9313 (tp30) cc_final: 0.9049 (tp30) REVERT: D 595 ILE cc_start: 0.9516 (tp) cc_final: 0.9313 (tp) REVERT: D 610 TRP cc_start: 0.7586 (p90) cc_final: 0.7208 (p90) REVERT: D 626 MET cc_start: 0.9453 (mmp) cc_final: 0.9224 (tpp) REVERT: D 650 GLN cc_start: 0.8631 (tp-100) cc_final: 0.7625 (tp-100) REVERT: E 69 TRP cc_start: 0.8776 (m-90) cc_final: 0.8540 (m-90) REVERT: E 100 MET cc_start: 0.9532 (ptm) cc_final: 0.9161 (ppp) REVERT: E 103 GLN cc_start: 0.9274 (tp40) cc_final: 0.8730 (tp-100) REVERT: E 165 LEU cc_start: 0.9551 (tp) cc_final: 0.9241 (tt) REVERT: E 279 ASN cc_start: 0.8899 (t0) cc_final: 0.8394 (t0) REVERT: E 434 MET cc_start: 0.8415 (mtt) cc_final: 0.8169 (mtt) REVERT: E 453 ILE cc_start: 0.8718 (mm) cc_final: 0.8447 (tp) REVERT: E 478 ASN cc_start: 0.9068 (t0) cc_final: 0.8656 (t0) REVERT: E 479 TRP cc_start: 0.9156 (m-90) cc_final: 0.8398 (m-90) REVERT: E 483 LEU cc_start: 0.9522 (mt) cc_final: 0.9276 (mm) REVERT: F 545 LEU cc_start: 0.9212 (tp) cc_final: 0.8884 (tp) REVERT: F 607 ASN cc_start: 0.8915 (p0) cc_final: 0.8670 (p0) REVERT: F 633 LYS cc_start: 0.9640 (mttt) cc_final: 0.9307 (mmmt) REVERT: F 650 GLN cc_start: 0.7437 (tp40) cc_final: 0.7113 (tp-100) REVERT: F 655 LYS cc_start: 0.9632 (ttmm) cc_final: 0.8942 (ttmm) REVERT: H 18 LEU cc_start: 0.8787 (tp) cc_final: 0.8509 (tp) REVERT: H 34 MET cc_start: 0.9609 (mmp) cc_final: 0.9275 (mmm) REVERT: H 45 LEU cc_start: 0.9646 (mm) cc_final: 0.9222 (mm) REVERT: H 82 MET cc_start: 0.9370 (ptt) cc_final: 0.9025 (tpt) REVERT: H 91 PHE cc_start: 0.9004 (m-80) cc_final: 0.8093 (m-80) REVERT: L 23 CYS cc_start: 0.4659 (p) cc_final: 0.3338 (p) REVERT: L 35 TRP cc_start: 0.8122 (m100) cc_final: 0.7053 (m100) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1060 time to fit residues: 28.6790 Evaluate side-chains 128 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 91 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN F 570 HIS F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.038943 restraints weight = 97774.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.040551 restraints weight = 58070.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.041711 restraints weight = 40566.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.042542 restraints weight = 31389.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.043150 restraints weight = 26045.645| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17295 Z= 0.123 Angle : 0.632 12.324 23679 Z= 0.309 Chirality : 0.045 0.258 2913 Planarity : 0.004 0.056 2833 Dihedral : 6.774 57.089 4264 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.19), residues: 1918 helix: 0.50 (0.27), residues: 399 sheet: -0.31 (0.22), residues: 557 loop : -0.62 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 186 TYR 0.018 0.001 TYR E 217 PHE 0.011 0.001 PHE L 98 TRP 0.036 0.002 TRP A 69 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00268 (17156) covalent geometry : angle 0.58596 (23296) SS BOND : bond 0.00298 ( 34) SS BOND : angle 0.92980 ( 68) hydrogen bonds : bond 0.03812 ( 480) hydrogen bonds : angle 5.34273 ( 1245) link_ALPHA1-3 : bond 0.00732 ( 5) link_ALPHA1-3 : angle 2.35267 ( 15) link_ALPHA1-6 : bond 0.01221 ( 4) link_ALPHA1-6 : angle 1.26555 ( 12) link_BETA1-4 : bond 0.00546 ( 36) link_BETA1-4 : angle 2.04365 ( 108) link_NAG-ASN : bond 0.00384 ( 60) link_NAG-ASN : angle 2.15105 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8608 (ptp) cc_final: 0.8356 (ptt) REVERT: A 201 ILE cc_start: 0.9415 (mp) cc_final: 0.8883 (tp) REVERT: A 425 ASN cc_start: 0.7860 (p0) cc_final: 0.7453 (p0) REVERT: A 494 LEU cc_start: 0.8750 (mt) cc_final: 0.8017 (mt) REVERT: B 528 SER cc_start: 0.9276 (m) cc_final: 0.8671 (p) REVERT: B 536 THR cc_start: 0.8970 (m) cc_final: 0.8760 (p) REVERT: B 601 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7278 (mtmm) REVERT: B 626 MET cc_start: 0.8211 (mmp) cc_final: 0.7866 (mmm) REVERT: B 648 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9200 (tm-30) REVERT: B 655 LYS cc_start: 0.9305 (pttp) cc_final: 0.9094 (pptt) REVERT: C 100 MET cc_start: 0.8361 (mmm) cc_final: 0.8104 (tpt) REVERT: C 104 MET cc_start: 0.8947 (ttm) cc_final: 0.8587 (ttt) REVERT: C 150 MET cc_start: 0.9240 (mmp) cc_final: 0.8881 (mmp) REVERT: C 434 MET cc_start: 0.7628 (ppp) cc_final: 0.7394 (ppp) REVERT: C 475 MET cc_start: 0.8780 (mmp) cc_final: 0.8563 (mmm) REVERT: D 535 MET cc_start: 0.9024 (mmp) cc_final: 0.8802 (mmp) REVERT: D 584 GLU cc_start: 0.9300 (tp30) cc_final: 0.9057 (tp30) REVERT: D 610 TRP cc_start: 0.7545 (p90) cc_final: 0.7297 (p90) REVERT: D 626 MET cc_start: 0.9464 (mmp) cc_final: 0.9231 (tpp) REVERT: D 650 GLN cc_start: 0.8638 (tp-100) cc_final: 0.7796 (tp-100) REVERT: E 69 TRP cc_start: 0.8754 (m-90) cc_final: 0.8223 (m-90) REVERT: E 100 MET cc_start: 0.9534 (ptm) cc_final: 0.9121 (ppp) REVERT: E 103 GLN cc_start: 0.9238 (tp40) cc_final: 0.8592 (tp-100) REVERT: E 104 MET cc_start: 0.9387 (mmt) cc_final: 0.9144 (mmp) REVERT: E 165 LEU cc_start: 0.9517 (tp) cc_final: 0.9211 (tt) REVERT: E 279 ASN cc_start: 0.8757 (t0) cc_final: 0.8217 (t0) REVERT: E 434 MET cc_start: 0.8335 (mtt) cc_final: 0.8081 (mtt) REVERT: E 453 ILE cc_start: 0.8684 (mm) cc_final: 0.8417 (tp) REVERT: E 478 ASN cc_start: 0.9048 (t0) cc_final: 0.8649 (t0) REVERT: E 479 TRP cc_start: 0.9136 (m-90) cc_final: 0.8490 (m-90) REVERT: E 483 LEU cc_start: 0.9505 (mt) cc_final: 0.9244 (mm) REVERT: F 545 LEU cc_start: 0.9196 (tp) cc_final: 0.8907 (tp) REVERT: F 607 ASN cc_start: 0.8845 (p0) cc_final: 0.8607 (p0) REVERT: F 633 LYS cc_start: 0.9625 (mttt) cc_final: 0.9306 (mmmt) REVERT: F 650 GLN cc_start: 0.7112 (tp40) cc_final: 0.6192 (tm-30) REVERT: F 654 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8960 (mt-10) REVERT: F 655 LYS cc_start: 0.9553 (ttmm) cc_final: 0.8927 (ttmm) REVERT: H 34 MET cc_start: 0.9527 (mmp) cc_final: 0.9133 (mmm) REVERT: H 45 LEU cc_start: 0.9474 (mm) cc_final: 0.9120 (mm) REVERT: H 76 ASP cc_start: 0.8133 (m-30) cc_final: 0.7810 (t0) REVERT: H 82 MET cc_start: 0.9342 (ptt) cc_final: 0.8939 (tpt) REVERT: L 23 CYS cc_start: 0.4649 (p) cc_final: 0.3783 (p) REVERT: L 35 TRP cc_start: 0.7996 (m100) cc_final: 0.7017 (m100) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1055 time to fit residues: 30.1027 Evaluate side-chains 132 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 49 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 650 GLN D 651 ASN F 570 HIS F 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.036669 restraints weight = 102174.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.038102 restraints weight = 62761.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039132 restraints weight = 44802.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.039864 restraints weight = 35317.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040407 restraints weight = 29756.955| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17295 Z= 0.259 Angle : 0.781 9.548 23679 Z= 0.383 Chirality : 0.047 0.330 2913 Planarity : 0.005 0.054 2833 Dihedral : 7.302 58.222 4264 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.19), residues: 1918 helix: 0.13 (0.26), residues: 399 sheet: -0.55 (0.22), residues: 526 loop : -0.76 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 186 TYR 0.039 0.002 TYR D 638 PHE 0.017 0.002 PHE F 522 TRP 0.048 0.003 TRP A 69 HIS 0.008 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00552 (17156) covalent geometry : angle 0.73791 (23296) SS BOND : bond 0.00397 ( 34) SS BOND : angle 1.21044 ( 68) hydrogen bonds : bond 0.04320 ( 480) hydrogen bonds : angle 5.74602 ( 1245) link_ALPHA1-3 : bond 0.00429 ( 5) link_ALPHA1-3 : angle 2.59404 ( 15) link_ALPHA1-6 : bond 0.01033 ( 4) link_ALPHA1-6 : angle 1.57580 ( 12) link_BETA1-4 : bond 0.00493 ( 36) link_BETA1-4 : angle 2.26525 ( 108) link_NAG-ASN : bond 0.00485 ( 60) link_NAG-ASN : angle 2.30453 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.19 seconds wall clock time: 37 minutes 33.86 seconds (2253.86 seconds total)