Starting phenix.real_space_refine on Mon Jun 23 14:34:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybh_33721/06_2025/7ybh_33721.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.067 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 114 5.16 5 C 17099 2.51 5 N 4366 2.21 5 O 5385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26964 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8596 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1046} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 8578 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1101, 8578 Classifications: {'peptide': 1101} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 8497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8497 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 58, 'TRANS': 1032} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 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: 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: "G" 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: "H" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "e" 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: "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: 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: "h" 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 17.16, per 1000 atoms: 0.64 Number of scatterers: 26964 At special positions: 0 Unit cell: (157.29, 147.66, 219.35, 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 114 16.00 O 5385 8.00 N 4366 7.00 C 17099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 642 " distance=2.02 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.04 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 833 " - pdb=" SG CYS A 844 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 583 " distance=2.07 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 664 " distance=2.04 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.04 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 J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 275 " " NAG A1306 " - " ASN A 596 " " NAG A1307 " - " ASN A 650 " " NAG A1308 " - " ASN A 609 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 336 " " NAG B1303 " - " ASN B 596 " " NAG B1304 " - " ASN B 650 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 324 " " NAG C1304 " - " ASN C 596 " " NAG C1305 " - " ASN C 650 " " NAG D 1 " - " ASN A 336 " " NAG E 1 " - " ASN A 702 " " NAG G 1 " - " ASN A 710 " " NAG H 1 " - " ASN A 794 " " NAG I 1 " - " ASN A1067 " " NAG J 1 " - " ASN A1091 " " NAG K 1 " - " ASN A1127 " " NAG L 1 " - " ASN B 324 " " NAG M 1 " - " ASN B 702 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 275 " " NAG R 1 " - " ASN B 609 " " NAG S 1 " - " ASN B 710 " " NAG T 1 " - " ASN B 794 " " NAG U 1 " - " ASN B1067 " " NAG V 1 " - " ASN B1091 " " NAG W 1 " - " ASN B1127 " " NAG X 1 " - " ASN C 275 " " NAG Y 1 " - " ASN C 336 " " NAG Z 1 " - " ASN C 702 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 609 " " NAG d 1 " - " ASN C 710 " " NAG e 1 " - " ASN C 794 " " NAG f 1 " - " ASN C1067 " " NAG g 1 " - " ASN C1091 " " NAG h 1 " - " ASN C1127 " Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 3.1 seconds 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 43 sheets defined 26.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 376 through 383 removed outlier: 5.095A pdb=" N ASN A 381 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 5.334A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 404 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.655A pdb=" N VAL A 613 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 747 Processing helix chain 'A' and resid 752 through 776 removed outlier: 3.697A pdb=" N ASP A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 Processing helix chain 'A' and resid 823 through 828 removed outlier: 4.057A pdb=" N ILE A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 829 through 835 Processing helix chain 'A' and resid 843 through 849 removed outlier: 3.615A pdb=" N ASN A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.536A pdb=" N GLY A 882 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.600A pdb=" N GLN A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 934 removed outlier: 3.731A pdb=" N TYR A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.452A pdb=" N VAL A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 976 removed outlier: 3.633A pdb=" N ILE A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1026 removed outlier: 4.026A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1154 removed outlier: 4.156A pdb=" N GLU A1137 " --> pdb=" O PRO A1133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A1154 " --> pdb=" O LYS A1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.818A pdb=" N VAL B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.632A pdb=" N TRP B 346 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.867A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.542A pdb=" N ASN B 381 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 4.573A pdb=" N ARG B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.568A pdb=" N ASN B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 619 through 622 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.935A pdb=" N TYR B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 751 through 776 removed outlier: 3.680A pdb=" N GLN B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 859 through 878 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.095A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.578A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 3.614A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 959 removed outlier: 4.393A pdb=" N VAL B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 977 removed outlier: 3.794A pdb=" N ILE B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.918A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1111 No H-bonds generated for 'chain 'B' and resid 1109 through 1111' Processing helix chain 'B' and resid 1133 through 1154 removed outlier: 4.024A pdb=" N SER B1154 " --> pdb=" O LYS B1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.680A pdb=" N LEU C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.621A pdb=" N TRP C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 4.380A pdb=" N LEU C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 4.151A pdb=" N ASN C 381 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 4.424A pdb=" N ARG C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 404 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 731 through 737 Processing helix chain 'C' and resid 740 through 746 Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 751 through 776 removed outlier: 3.949A pdb=" N ASN C 757 " --> pdb=" O CYS C 753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 768 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 819 Processing helix chain 'C' and resid 859 through 878 removed outlier: 3.580A pdb=" N GLY C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 883 removed outlier: 3.920A pdb=" N GLY C 882 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 removed outlier: 3.781A pdb=" N ILE C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.517A pdb=" N TYR C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 934 removed outlier: 3.686A pdb=" N ILE C 927 " --> pdb=" O ALA C 923 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 934 " --> pdb=" O SER C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.090A pdb=" N VAL C 944 " --> pdb=" O LYS C 940 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 969 through 975 removed outlier: 3.603A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 984 through 1026 removed outlier: 3.674A pdb=" N VAL C1026 " --> pdb=" O MET C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1154 removed outlier: 4.304A pdb=" N SER C1154 " --> pdb=" O LYS C1150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.033A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 257 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 95 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.074A pdb=" N ASP A 280 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.935A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.355A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 312 removed outlier: 5.323A pdb=" N ASN A 310 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 586 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY A 587 " --> pdb=" O GLN A 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 606 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 321 removed outlier: 5.680A pdb=" N ASP A 567 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 558 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.146A pdb=" N ASN A 387 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 425 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.660A pdb=" N GLU A 647 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 695 removed outlier: 6.524A pdb=" N ALA A 694 " --> pdb=" O ILE C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 704 through 708 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 721 removed outlier: 6.940A pdb=" N GLY A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER A1048 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1054 " --> pdb=" O PRO A1046 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A1056 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A1044 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A1058 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1113 through 1118 removed outlier: 5.487A pdb=" N VAL A1115 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A1082 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A1117 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1074 " --> pdb=" O HIS A1081 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR B 262 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 257 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 95 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.970A pdb=" N ASP B 280 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.114A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 141 through 144 removed outlier: 6.722A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.832A pdb=" N GLY B 304 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 592 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 317 through 321 removed outlier: 4.038A pdb=" N VAL B 532 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 543 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 347 through 351 Processing sheet with id=AC5, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AC6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'B' and resid 647 through 648 removed outlier: 5.726A pdb=" N GLU B 647 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR B 689 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA B 665 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 704 through 721 removed outlier: 6.454A pdb=" N SER B 704 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B1069 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 706 " --> pdb=" O ASN B1067 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B1067 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B1065 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B1052 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B1048 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1054 " --> pdb=" O PRO B1046 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1056 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER B1044 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B1058 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AD1, first strand: chain 'B' and resid 1080 through 1083 removed outlier: 3.800A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1087 through 1090 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.516A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA C 257 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 95 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 280 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.605A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 140 through 143 Processing sheet with id=AD7, first strand: chain 'C' and resid 306 through 312 removed outlier: 4.436A pdb=" N VAL C 588 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN C 310 " --> pdb=" O GLY C 586 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY C 586 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 587 " --> pdb=" O GLN C 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 321 Processing sheet with id=AD9, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.656A pdb=" N VAL C 388 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 removed outlier: 6.824A pdb=" N CYS C 354 " --> pdb=" O CYS C 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 445 through 447 Processing sheet with id=AE3, first strand: chain 'C' and resid 657 through 660 removed outlier: 6.498A pdb=" N ILE C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 721 removed outlier: 6.012A pdb=" N TYR C1060 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS C1041 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1069 through 1070 Processing sheet with id=AE7, first strand: chain 'C' and resid 1113 through 1118 removed outlier: 4.825A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1074 " --> pdb=" O HIS C1081 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2727 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: 12.78 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6897 1.33 - 1.46: 6893 1.46 - 1.58: 13633 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 27564 Sorted by residual: bond pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 ... (remaining 27559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 36959 2.62 - 5.24: 503 5.24 - 7.85: 48 7.85 - 10.47: 7 10.47 - 13.09: 14 Bond angle restraints: 37531 Sorted by residual: angle pdb=" CA PRO C 935 " pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 112.00 99.11 12.89 1.40e+00 5.10e-01 8.48e+01 angle pdb=" CA PRO B 935 " pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" CA PRO B 810 " pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO A 810 " pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.16e+01 angle pdb=" CA PRO A 892 " pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 ... (remaining 37526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 16165 22.08 - 44.17: 1104 44.17 - 66.25: 158 66.25 - 88.33: 169 88.33 - 110.42: 98 Dihedral angle restraints: 17694 sinusoidal: 8093 harmonic: 9601 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 1.98 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA CYS C 583 " pdb=" C CYS C 583 " pdb=" N SER C 584 " pdb=" CA SER C 584 " ideal model delta harmonic sigma weight residual -180.00 -137.49 -42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 17691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4386 0.112 - 0.224: 121 0.224 - 0.336: 20 0.336 - 0.447: 1 0.447 - 0.559: 1 Chirality restraints: 4529 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 324 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 324 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 702 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4526 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " 1.009 9.50e-02 1.11e+02 4.52e-01 1.24e+02 pdb=" NE ARG C 312 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.971 9.50e-02 1.11e+02 4.35e-01 1.14e+02 pdb=" NE ARG A 321 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 891 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO B 892 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " 0.080 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 168 2.51 - 3.11: 20298 3.11 - 3.70: 39300 3.70 - 4.30: 53018 4.30 - 4.90: 88947 Nonbonded interactions: 201731 Sorted by model distance: nonbonded pdb=" OG SER C 809 " pdb=" CD PRO C 810 " model vdw 1.909 3.440 nonbonded pdb=" O ASP C 283 " pdb=" OG SER C 290 " model vdw 2.064 3.040 nonbonded pdb=" OG SER A 809 " pdb=" OE1 GLU A 812 " model vdw 2.119 3.040 nonbonded pdb=" OG SER B 462 " pdb=" OE1 GLU B 464 " model vdw 2.147 3.040 nonbonded pdb=" O TYR C1040 " pdb=" OG1 THR C1059 " model vdw 2.149 3.040 ... (remaining 201726 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' and (resid 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 821 or (resid 846 and (name N o \ r name CA or name C or name O or name CB )) or resid 847 through 1155 or resid 1 \ 301 through 1304)) selection = (chain 'B' and (resid 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 616 or resid 634 through 842 or \ (resid 846 and (name N or name CA or name C or name O or name CB )) or resid 84 \ 7 through 1155 or resid 1301 through 1304)) selection = (chain 'C' and (resid 14 through 616 or resid 634 through 1155 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 65.850 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.005 0.062 27699 Z= 0.242 Angle : 0.796 13.088 37894 Z= 0.409 Chirality : 0.051 0.559 4529 Planarity : 0.012 0.452 4744 Dihedral : 18.854 110.416 11392 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 0.42 % Allowed : 0.45 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3271 helix: 0.98 (0.20), residues: 736 sheet: -0.04 (0.20), residues: 649 loop : -1.60 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 429 HIS 0.007 0.001 HIS A 245 PHE 0.030 0.002 PHE A 157 TYR 0.016 0.001 TYR A1060 ARG 0.013 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 45) link_NAG-ASN : angle 2.55455 ( 135) link_BETA1-4 : bond 0.00607 ( 47) link_BETA1-4 : angle 1.77232 ( 141) link_ALPHA1-3 : bond 0.00434 ( 1) link_ALPHA1-3 : angle 1.54093 ( 3) hydrogen bonds : bond 0.14661 ( 1002) hydrogen bonds : angle 6.72420 ( 2727) SS BOND : bond 0.00692 ( 42) SS BOND : angle 1.58785 ( 84) covalent geometry : bond 0.00480 (27564) covalent geometry : angle 0.77421 (37531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 482 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6831 (t0) cc_final: 0.6596 (t0) REVERT: A 577 ILE cc_start: 0.8285 (mm) cc_final: 0.7743 (mt) REVERT: B 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7747 (pp30) REVERT: B 177 MET cc_start: 0.7083 (pmm) cc_final: 0.4404 (mmm) REVERT: B 335 PHE cc_start: 0.8024 (m-80) cc_final: 0.7752 (m-80) REVERT: B 385 PHE cc_start: 0.6832 (m-80) cc_final: 0.5795 (m-80) REVERT: B 446 TYR cc_start: 0.8439 (p90) cc_final: 0.8238 (p90) REVERT: C 313 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8625 (t) REVERT: C 490 PHE cc_start: 0.4148 (m-80) cc_final: 0.3155 (m-80) REVERT: C 769 LYS cc_start: 0.8948 (tppp) cc_final: 0.8712 (tptm) outliers start: 12 outliers final: 5 residues processed: 494 average time/residue: 0.3600 time to fit residues: 284.6718 Evaluate side-chains 235 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 229 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 668 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B 948 ASN B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 121 ASN C 310 ASN C 491 GLN C 606 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.141554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101203 restraints weight = 71994.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.104319 restraints weight = 34700.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106282 restraints weight = 22828.519| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27699 Z= 0.266 Angle : 0.872 11.109 37894 Z= 0.427 Chirality : 0.053 0.421 4529 Planarity : 0.006 0.097 4744 Dihedral : 12.152 93.148 5522 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 1.85 % Allowed : 12.17 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3271 helix: 0.79 (0.19), residues: 747 sheet: -0.28 (0.21), residues: 593 loop : -1.82 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.010 0.002 HIS A 66 PHE 0.032 0.003 PHE A1141 TYR 0.025 0.002 TYR C 170 ARG 0.027 0.001 ARG B 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 45) link_NAG-ASN : angle 2.55951 ( 135) link_BETA1-4 : bond 0.00508 ( 47) link_BETA1-4 : angle 2.78105 ( 141) link_ALPHA1-3 : bond 0.00796 ( 1) link_ALPHA1-3 : angle 3.92687 ( 3) hydrogen bonds : bond 0.06289 ( 1002) hydrogen bonds : angle 5.83310 ( 2727) SS BOND : bond 0.00557 ( 42) SS BOND : angle 2.01308 ( 84) covalent geometry : bond 0.00609 (27564) covalent geometry : angle 0.83944 (37531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7885 (ptp90) cc_final: 0.7647 (ptp90) REVERT: A 577 ILE cc_start: 0.8427 (mm) cc_final: 0.7898 (mt) REVERT: A 895 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8687 (tpt) REVERT: A 971 ASN cc_start: 0.8846 (p0) cc_final: 0.8631 (p0) REVERT: B 21 ARG cc_start: 0.5714 (mtt180) cc_final: 0.5368 (mmm-85) REVERT: B 177 MET cc_start: 0.7327 (pmm) cc_final: 0.4682 (tpt) REVERT: B 449 PHE cc_start: 0.8319 (m-80) cc_final: 0.8035 (m-80) REVERT: B 972 ASP cc_start: 0.8274 (t0) cc_final: 0.7783 (t0) REVERT: C 168 PHE cc_start: 0.7558 (t80) cc_final: 0.6838 (t80) REVERT: C 449 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8129 (t80) REVERT: C 555 PHE cc_start: 0.7885 (p90) cc_final: 0.7409 (p90) REVERT: C 769 LYS cc_start: 0.9188 (tppp) cc_final: 0.8824 (tptm) outliers start: 53 outliers final: 33 residues processed: 296 average time/residue: 0.3656 time to fit residues: 178.4184 Evaluate side-chains 231 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 895 MET Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 287 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 180 optimal weight: 0.0870 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 126 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 66 HIS B 245 HIS B 443 ASN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.131375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092153 restraints weight = 71676.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.096583 restraints weight = 36932.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.096595 restraints weight = 20896.051| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27699 Z= 0.182 Angle : 0.710 9.897 37894 Z= 0.346 Chirality : 0.047 0.390 4529 Planarity : 0.004 0.069 4744 Dihedral : 9.791 92.340 5516 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 2.97 % Allowed : 14.09 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3271 helix: 1.27 (0.19), residues: 736 sheet: -0.24 (0.21), residues: 599 loop : -1.77 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 251 HIS 0.005 0.001 HIS C 245 PHE 0.024 0.002 PHE A 32 TYR 0.023 0.002 TYR A1060 ARG 0.009 0.001 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 45) link_NAG-ASN : angle 2.33093 ( 135) link_BETA1-4 : bond 0.00645 ( 47) link_BETA1-4 : angle 2.17304 ( 141) link_ALPHA1-3 : bond 0.01338 ( 1) link_ALPHA1-3 : angle 2.02914 ( 3) hydrogen bonds : bond 0.05726 ( 1002) hydrogen bonds : angle 5.48649 ( 2727) SS BOND : bond 0.00653 ( 42) SS BOND : angle 1.81151 ( 84) covalent geometry : bond 0.00428 (27564) covalent geometry : angle 0.68082 (37531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 215 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8538 (mm) cc_final: 0.7937 (mt) REVERT: A 1024 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: B 21 ARG cc_start: 0.5797 (mtt180) cc_final: 0.5302 (ttm170) REVERT: B 177 MET cc_start: 0.7047 (pmm) cc_final: 0.4414 (tpt) REVERT: B 331 PHE cc_start: 0.8702 (m-80) cc_final: 0.8453 (m-80) REVERT: B 373 TYR cc_start: 0.6744 (m-80) cc_final: 0.6281 (m-10) REVERT: B 446 TYR cc_start: 0.8539 (p90) cc_final: 0.7917 (p90) REVERT: B 449 PHE cc_start: 0.8392 (m-80) cc_final: 0.8112 (m-80) REVERT: B 893 MET cc_start: 0.8270 (mtt) cc_final: 0.7975 (mtp) REVERT: B 972 ASP cc_start: 0.8134 (t0) cc_final: 0.7770 (t0) REVERT: C 449 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8288 (t80) REVERT: C 511 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7161 (mm) REVERT: C 555 PHE cc_start: 0.7890 (p90) cc_final: 0.7433 (p90) REVERT: C 728 SER cc_start: 0.9430 (t) cc_final: 0.8877 (m) REVERT: C 769 LYS cc_start: 0.9185 (tppp) cc_final: 0.8800 (tptm) REVERT: C 866 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8905 (m-10) REVERT: C 987 ASP cc_start: 0.8213 (m-30) cc_final: 0.7988 (m-30) REVERT: C 1131 TYR cc_start: 0.8027 (t80) cc_final: 0.7781 (t80) outliers start: 85 outliers final: 43 residues processed: 282 average time/residue: 0.3275 time to fit residues: 156.6531 Evaluate side-chains 241 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 296 optimal weight: 0.1980 chunk 141 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 299 optimal weight: 0.6980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 829 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.129665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089646 restraints weight = 71738.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092651 restraints weight = 34568.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.094376 restraints weight = 22775.252| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27699 Z= 0.172 Angle : 0.692 9.597 37894 Z= 0.336 Chirality : 0.047 0.394 4529 Planarity : 0.004 0.065 4744 Dihedral : 8.600 86.453 5516 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 2.73 % Allowed : 16.01 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3271 helix: 1.49 (0.19), residues: 733 sheet: -0.33 (0.21), residues: 609 loop : -1.79 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 251 HIS 0.003 0.001 HIS B1051 PHE 0.024 0.002 PHE A 32 TYR 0.020 0.001 TYR C1060 ARG 0.005 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 45) link_NAG-ASN : angle 2.29668 ( 135) link_BETA1-4 : bond 0.00539 ( 47) link_BETA1-4 : angle 2.13246 ( 141) link_ALPHA1-3 : bond 0.01149 ( 1) link_ALPHA1-3 : angle 2.95624 ( 3) hydrogen bonds : bond 0.05420 ( 1002) hydrogen bonds : angle 5.35679 ( 2727) SS BOND : bond 0.00442 ( 42) SS BOND : angle 1.59558 ( 84) covalent geometry : bond 0.00398 (27564) covalent geometry : angle 0.66382 (37531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8663 (mm) cc_final: 0.8043 (mt) REVERT: A 733 MET cc_start: 0.8614 (tpp) cc_final: 0.8311 (mtp) REVERT: A 812 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: A 1022 MET cc_start: 0.8711 (tpp) cc_final: 0.8160 (ttm) REVERT: A 1024 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: A 1137 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6768 (mm-30) REVERT: B 21 ARG cc_start: 0.5697 (mtt180) cc_final: 0.5272 (ttm170) REVERT: B 56 LEU cc_start: 0.7585 (tt) cc_final: 0.7239 (tt) REVERT: B 177 MET cc_start: 0.6633 (pmm) cc_final: 0.4336 (tpt) REVERT: B 239 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: B 373 TYR cc_start: 0.7184 (m-80) cc_final: 0.6952 (m-10) REVERT: B 417 LYS cc_start: 0.7734 (tppt) cc_final: 0.7425 (tppt) REVERT: B 426 VAL cc_start: 0.8550 (t) cc_final: 0.8285 (p) REVERT: B 446 TYR cc_start: 0.8503 (p90) cc_final: 0.7862 (p90) REVERT: B 449 PHE cc_start: 0.8441 (m-80) cc_final: 0.7965 (m-80) REVERT: B 466 TYR cc_start: 0.7873 (t80) cc_final: 0.7487 (t80) REVERT: B 893 MET cc_start: 0.8359 (mtt) cc_final: 0.8011 (mtp) REVERT: B 972 ASP cc_start: 0.8283 (t0) cc_final: 0.8014 (t0) REVERT: C 224 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: C 449 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8153 (t80) REVERT: C 555 PHE cc_start: 0.7879 (p90) cc_final: 0.7403 (p90) REVERT: C 728 SER cc_start: 0.9430 (t) cc_final: 0.8884 (m) REVERT: C 769 LYS cc_start: 0.9176 (tppp) cc_final: 0.8800 (tptm) REVERT: C 866 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.8995 (m-10) REVERT: C 987 ASP cc_start: 0.8141 (m-30) cc_final: 0.7915 (m-30) REVERT: C 1131 TYR cc_start: 0.7971 (t80) cc_final: 0.7608 (t80) outliers start: 78 outliers final: 47 residues processed: 266 average time/residue: 0.3748 time to fit residues: 168.8480 Evaluate side-chains 229 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 188 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.131432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090247 restraints weight = 72004.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093213 restraints weight = 35382.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094907 restraints weight = 23354.479| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27699 Z= 0.190 Angle : 0.705 12.774 37894 Z= 0.345 Chirality : 0.047 0.401 4529 Planarity : 0.004 0.047 4744 Dihedral : 8.202 82.891 5516 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.46 % Rotamer: Outliers : 3.60 % Allowed : 16.82 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3271 helix: 1.46 (0.19), residues: 737 sheet: -0.37 (0.21), residues: 624 loop : -1.80 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 251 HIS 0.004 0.001 HIS B1051 PHE 0.022 0.002 PHE A 32 TYR 0.021 0.001 TYR C1060 ARG 0.008 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 45) link_NAG-ASN : angle 2.37117 ( 135) link_BETA1-4 : bond 0.00592 ( 47) link_BETA1-4 : angle 1.93836 ( 141) link_ALPHA1-3 : bond 0.01267 ( 1) link_ALPHA1-3 : angle 2.41731 ( 3) hydrogen bonds : bond 0.05677 ( 1002) hydrogen bonds : angle 5.36939 ( 2727) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.65850 ( 84) covalent geometry : bond 0.00444 (27564) covalent geometry : angle 0.67934 (37531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 197 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4585 (m-80) cc_final: 0.4381 (t80) REVERT: A 228 ASP cc_start: 0.8213 (p0) cc_final: 0.7949 (p0) REVERT: A 461 ILE cc_start: 0.3678 (OUTLIER) cc_final: 0.3437 (pt) REVERT: A 577 ILE cc_start: 0.8669 (mm) cc_final: 0.8079 (mt) REVERT: A 692 LEU cc_start: 0.9061 (mt) cc_final: 0.8841 (mt) REVERT: A 812 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 1022 MET cc_start: 0.8774 (tpp) cc_final: 0.8217 (ttm) REVERT: A 1024 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: B 21 ARG cc_start: 0.5459 (mtt180) cc_final: 0.4915 (ttm170) REVERT: B 56 LEU cc_start: 0.7622 (tt) cc_final: 0.7387 (tt) REVERT: B 177 MET cc_start: 0.6170 (pmm) cc_final: 0.4300 (tpt) REVERT: B 373 TYR cc_start: 0.7566 (m-80) cc_final: 0.7326 (m-10) REVERT: B 417 LYS cc_start: 0.7925 (tppt) cc_final: 0.7617 (tppt) REVERT: B 446 TYR cc_start: 0.8551 (p90) cc_final: 0.7942 (p90) REVERT: B 449 PHE cc_start: 0.8433 (m-80) cc_final: 0.7919 (m-80) REVERT: B 466 TYR cc_start: 0.7874 (t80) cc_final: 0.7520 (t80) REVERT: B 893 MET cc_start: 0.8469 (mtt) cc_final: 0.8158 (mtp) REVERT: B 972 ASP cc_start: 0.8398 (t0) cc_final: 0.8163 (t0) REVERT: C 224 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: C 449 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8425 (t80) REVERT: C 461 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 555 PHE cc_start: 0.7915 (p90) cc_final: 0.7407 (p90) REVERT: C 728 SER cc_start: 0.9467 (t) cc_final: 0.8892 (m) REVERT: C 769 LYS cc_start: 0.9182 (tppp) cc_final: 0.8811 (tptm) REVERT: C 866 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8928 (m-10) REVERT: C 987 ASP cc_start: 0.8177 (m-30) cc_final: 0.7916 (m-30) REVERT: C 1131 TYR cc_start: 0.7864 (t80) cc_final: 0.7581 (t80) outliers start: 103 outliers final: 68 residues processed: 279 average time/residue: 0.3485 time to fit residues: 166.6437 Evaluate side-chains 252 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 304 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 323 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.127381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087137 restraints weight = 66787.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089798 restraints weight = 34772.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091570 restraints weight = 23586.106| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27699 Z= 0.156 Angle : 0.677 10.854 37894 Z= 0.329 Chirality : 0.046 0.394 4529 Planarity : 0.004 0.050 4744 Dihedral : 7.687 77.640 5516 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 3.53 % Allowed : 17.59 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3271 helix: 1.56 (0.20), residues: 739 sheet: -0.24 (0.21), residues: 642 loop : -1.78 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS B 648 PHE 0.026 0.001 PHE C 168 TYR 0.019 0.001 TYR C1060 ARG 0.006 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 45) link_NAG-ASN : angle 2.30412 ( 135) link_BETA1-4 : bond 0.00559 ( 47) link_BETA1-4 : angle 1.94686 ( 141) link_ALPHA1-3 : bond 0.00871 ( 1) link_ALPHA1-3 : angle 2.32277 ( 3) hydrogen bonds : bond 0.05301 ( 1002) hydrogen bonds : angle 5.27687 ( 2727) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.50907 ( 84) covalent geometry : bond 0.00361 (27564) covalent geometry : angle 0.65064 (37531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 194 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.3710 (OUTLIER) cc_final: 0.3406 (pt) REVERT: A 812 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: A 1022 MET cc_start: 0.8670 (tpp) cc_final: 0.7994 (ttm) REVERT: A 1024 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: A 1137 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6672 (mm-30) REVERT: B 21 ARG cc_start: 0.5444 (mtt180) cc_final: 0.4891 (ttm170) REVERT: B 52 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 177 MET cc_start: 0.6104 (pmm) cc_final: 0.4490 (tpt) REVERT: B 373 TYR cc_start: 0.7488 (m-80) cc_final: 0.7188 (m-10) REVERT: B 446 TYR cc_start: 0.8510 (p90) cc_final: 0.8007 (p90) REVERT: B 449 PHE cc_start: 0.8338 (m-80) cc_final: 0.7910 (m-80) REVERT: B 466 TYR cc_start: 0.7623 (t80) cc_final: 0.7207 (t80) REVERT: B 508 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7554 (p90) REVERT: B 893 MET cc_start: 0.8142 (mtt) cc_final: 0.7855 (mtp) REVERT: C 224 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: C 461 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 555 PHE cc_start: 0.7761 (p90) cc_final: 0.7389 (p90) REVERT: C 728 SER cc_start: 0.9372 (t) cc_final: 0.8856 (m) REVERT: C 769 LYS cc_start: 0.9141 (tppp) cc_final: 0.8835 (tptm) REVERT: C 866 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8896 (m-10) REVERT: C 987 ASP cc_start: 0.7946 (m-30) cc_final: 0.7745 (m-30) outliers start: 101 outliers final: 73 residues processed: 272 average time/residue: 0.4416 time to fit residues: 203.6696 Evaluate side-chains 257 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 286 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 60 optimal weight: 0.1980 chunk 241 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.0070 chunk 235 optimal weight: 0.0070 chunk 194 optimal weight: 0.0670 chunk 42 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 GLN A1003 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.132386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092944 restraints weight = 67481.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096843 restraints weight = 36418.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096892 restraints weight = 20776.213| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27699 Z= 0.113 Angle : 0.646 15.564 37894 Z= 0.312 Chirality : 0.045 0.369 4529 Planarity : 0.004 0.052 4744 Dihedral : 6.909 71.331 5516 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 2.73 % Allowed : 18.53 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3271 helix: 1.65 (0.20), residues: 742 sheet: -0.07 (0.21), residues: 627 loop : -1.60 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 251 HIS 0.008 0.001 HIS C 648 PHE 0.023 0.001 PHE C 168 TYR 0.020 0.001 TYR A1131 ARG 0.005 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 45) link_NAG-ASN : angle 2.14672 ( 135) link_BETA1-4 : bond 0.00605 ( 47) link_BETA1-4 : angle 1.82372 ( 141) link_ALPHA1-3 : bond 0.01186 ( 1) link_ALPHA1-3 : angle 1.98527 ( 3) hydrogen bonds : bond 0.04284 ( 1002) hydrogen bonds : angle 4.99950 ( 2727) SS BOND : bond 0.00297 ( 42) SS BOND : angle 1.13883 ( 84) covalent geometry : bond 0.00240 (27564) covalent geometry : angle 0.62420 (37531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 202 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4106 (OUTLIER) cc_final: 0.3882 (t80) REVERT: A 461 ILE cc_start: 0.3833 (OUTLIER) cc_final: 0.3488 (pt) REVERT: A 812 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 1137 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6699 (mm-30) REVERT: B 21 ARG cc_start: 0.5729 (mtt180) cc_final: 0.5093 (tpp80) REVERT: B 177 MET cc_start: 0.6162 (pmm) cc_final: 0.4350 (tpt) REVERT: B 446 TYR cc_start: 0.8491 (p90) cc_final: 0.7967 (p90) REVERT: B 449 PHE cc_start: 0.8393 (m-80) cc_final: 0.7945 (m-80) REVERT: B 466 TYR cc_start: 0.7834 (t80) cc_final: 0.7420 (t80) REVERT: B 874 THR cc_start: 0.8244 (m) cc_final: 0.8011 (m) REVERT: B 893 MET cc_start: 0.7889 (mtt) cc_final: 0.7590 (mtp) REVERT: C 51 THR cc_start: 0.8780 (t) cc_final: 0.8478 (p) REVERT: C 449 PHE cc_start: 0.8292 (t80) cc_final: 0.7387 (t80) REVERT: C 461 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7485 (mt) REVERT: C 466 TYR cc_start: 0.7445 (t80) cc_final: 0.6673 (t80) REVERT: C 477 GLU cc_start: 0.6399 (tp30) cc_final: 0.5861 (pp20) REVERT: C 555 PHE cc_start: 0.7698 (p90) cc_final: 0.7332 (p90) REVERT: C 728 SER cc_start: 0.9310 (t) cc_final: 0.8851 (m) REVERT: C 769 LYS cc_start: 0.9143 (tppp) cc_final: 0.8855 (tptp) REVERT: C 987 ASP cc_start: 0.8061 (m-30) cc_final: 0.7858 (m-30) outliers start: 78 outliers final: 45 residues processed: 255 average time/residue: 0.3663 time to fit residues: 156.6285 Evaluate side-chains 225 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 274 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 328 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 169 optimal weight: 0.0980 chunk 166 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN C 770 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.132603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092601 restraints weight = 68151.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096660 restraints weight = 38433.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096574 restraints weight = 22519.395| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27699 Z= 0.202 Angle : 0.723 17.849 37894 Z= 0.349 Chirality : 0.046 0.393 4529 Planarity : 0.004 0.051 4744 Dihedral : 7.012 63.394 5515 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 2.45 % Allowed : 19.48 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3271 helix: 1.56 (0.19), residues: 741 sheet: -0.20 (0.20), residues: 639 loop : -1.75 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 251 HIS 0.008 0.001 HIS C 648 PHE 0.025 0.002 PHE A 32 TYR 0.034 0.002 TYR A 416 ARG 0.008 0.001 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 45) link_NAG-ASN : angle 2.35670 ( 135) link_BETA1-4 : bond 0.00534 ( 47) link_BETA1-4 : angle 1.90608 ( 141) link_ALPHA1-3 : bond 0.01078 ( 1) link_ALPHA1-3 : angle 2.17743 ( 3) hydrogen bonds : bond 0.05549 ( 1002) hydrogen bonds : angle 5.26521 ( 2727) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.53073 ( 84) covalent geometry : bond 0.00477 (27564) covalent geometry : angle 0.69891 (37531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4114 (OUTLIER) cc_final: 0.3881 (t80) REVERT: A 461 ILE cc_start: 0.3752 (OUTLIER) cc_final: 0.3365 (pt) REVERT: A 812 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: A 1137 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6849 (mm-30) REVERT: B 21 ARG cc_start: 0.5653 (mtt180) cc_final: 0.4986 (tpp80) REVERT: B 177 MET cc_start: 0.6182 (pmm) cc_final: 0.4503 (tpt) REVERT: B 417 LYS cc_start: 0.7615 (tttt) cc_final: 0.7294 (tptt) REVERT: B 446 TYR cc_start: 0.8451 (p90) cc_final: 0.7939 (p90) REVERT: B 449 PHE cc_start: 0.8359 (m-80) cc_final: 0.7877 (m-80) REVERT: B 466 TYR cc_start: 0.7757 (t80) cc_final: 0.7343 (t80) REVERT: B 512 HIS cc_start: 0.6933 (p90) cc_final: 0.6556 (p90) REVERT: B 893 MET cc_start: 0.8251 (mtt) cc_final: 0.7997 (mtp) REVERT: C 51 THR cc_start: 0.8819 (t) cc_final: 0.8554 (p) REVERT: C 449 PHE cc_start: 0.8281 (t80) cc_final: 0.7708 (t80) REVERT: C 461 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7482 (mt) REVERT: C 477 GLU cc_start: 0.6387 (tp30) cc_final: 0.5835 (pp20) REVERT: C 555 PHE cc_start: 0.7795 (p90) cc_final: 0.7402 (p90) REVERT: C 769 LYS cc_start: 0.9184 (tppp) cc_final: 0.8915 (tptm) REVERT: C 987 ASP cc_start: 0.8053 (m-30) cc_final: 0.7819 (m-30) outliers start: 70 outliers final: 56 residues processed: 236 average time/residue: 0.3530 time to fit residues: 139.5955 Evaluate side-chains 227 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 192 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 142 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 995 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089226 restraints weight = 66790.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091985 restraints weight = 34119.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093823 restraints weight = 22871.854| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27699 Z= 0.114 Angle : 0.656 15.367 37894 Z= 0.315 Chirality : 0.045 0.377 4529 Planarity : 0.004 0.053 4744 Dihedral : 6.485 59.320 5515 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 2.03 % Allowed : 19.90 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3271 helix: 1.70 (0.20), residues: 743 sheet: -0.07 (0.21), residues: 609 loop : -1.61 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 251 HIS 0.008 0.001 HIS C 648 PHE 0.027 0.001 PHE B 816 TYR 0.026 0.001 TYR B 170 ARG 0.008 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.13666 ( 135) link_BETA1-4 : bond 0.00579 ( 47) link_BETA1-4 : angle 1.76702 ( 141) link_ALPHA1-3 : bond 0.00942 ( 1) link_ALPHA1-3 : angle 1.91082 ( 3) hydrogen bonds : bond 0.04588 ( 1002) hydrogen bonds : angle 5.02726 ( 2727) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.16602 ( 84) covalent geometry : bond 0.00251 (27564) covalent geometry : angle 0.63439 (37531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4119 (OUTLIER) cc_final: 0.3906 (t80) REVERT: A 461 ILE cc_start: 0.4041 (OUTLIER) cc_final: 0.3666 (pt) REVERT: A 812 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: A 1137 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6742 (mm-30) REVERT: B 21 ARG cc_start: 0.5855 (mtt180) cc_final: 0.5290 (tpp80) REVERT: B 177 MET cc_start: 0.6171 (pmm) cc_final: 0.4417 (tpt) REVERT: B 417 LYS cc_start: 0.7369 (tttt) cc_final: 0.7153 (tptt) REVERT: B 446 TYR cc_start: 0.8462 (p90) cc_final: 0.8037 (p90) REVERT: B 449 PHE cc_start: 0.8242 (m-80) cc_final: 0.7854 (m-80) REVERT: B 466 TYR cc_start: 0.7703 (t80) cc_final: 0.7277 (t80) REVERT: B 874 THR cc_start: 0.8261 (m) cc_final: 0.8015 (m) REVERT: B 893 MET cc_start: 0.8023 (mtt) cc_final: 0.7706 (mtp) REVERT: C 51 THR cc_start: 0.8797 (t) cc_final: 0.8525 (p) REVERT: C 449 PHE cc_start: 0.7917 (t80) cc_final: 0.7234 (t80) REVERT: C 461 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7562 (mt) REVERT: C 466 TYR cc_start: 0.7352 (t80) cc_final: 0.6367 (t80) REVERT: C 477 GLU cc_start: 0.6134 (tp30) cc_final: 0.5737 (pp20) REVERT: C 511 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7182 (mm) REVERT: C 555 PHE cc_start: 0.7646 (p90) cc_final: 0.7328 (p90) REVERT: C 769 LYS cc_start: 0.9136 (tppp) cc_final: 0.8850 (tptm) outliers start: 58 outliers final: 48 residues processed: 230 average time/residue: 0.3340 time to fit residues: 130.6719 Evaluate side-chains 234 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091334 restraints weight = 66907.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095278 restraints weight = 36749.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095373 restraints weight = 21000.643| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 27699 Z= 0.142 Angle : 0.765 59.121 37894 Z= 0.398 Chirality : 0.045 0.534 4529 Planarity : 0.004 0.053 4744 Dihedral : 6.478 59.350 5515 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 2.06 % Allowed : 19.93 % Favored : 78.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3271 helix: 1.68 (0.20), residues: 743 sheet: -0.00 (0.21), residues: 621 loop : -1.60 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 251 HIS 0.007 0.001 HIS C 648 PHE 0.025 0.001 PHE B1045 TYR 0.016 0.001 TYR C1060 ARG 0.006 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 45) link_NAG-ASN : angle 2.13862 ( 135) link_BETA1-4 : bond 0.00579 ( 47) link_BETA1-4 : angle 1.76904 ( 141) link_ALPHA1-3 : bond 0.00274 ( 1) link_ALPHA1-3 : angle 1.72880 ( 3) hydrogen bonds : bond 0.04610 ( 1002) hydrogen bonds : angle 5.02921 ( 2727) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.16960 ( 84) covalent geometry : bond 0.00314 (27564) covalent geometry : angle 0.74750 (37531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4153 (OUTLIER) cc_final: 0.3880 (t80) REVERT: A 461 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3709 (pt) REVERT: A 812 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: A 1137 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6775 (mm-30) REVERT: B 21 ARG cc_start: 0.5857 (mtt180) cc_final: 0.5210 (tpp80) REVERT: B 177 MET cc_start: 0.6138 (pmm) cc_final: 0.4345 (tpt) REVERT: B 417 LYS cc_start: 0.7479 (tttt) cc_final: 0.7160 (tptt) REVERT: B 446 TYR cc_start: 0.8454 (p90) cc_final: 0.7976 (p90) REVERT: B 449 PHE cc_start: 0.8336 (m-80) cc_final: 0.7895 (m-80) REVERT: B 466 TYR cc_start: 0.7806 (t80) cc_final: 0.7415 (t80) REVERT: B 874 THR cc_start: 0.8280 (m) cc_final: 0.8003 (m) REVERT: B 893 MET cc_start: 0.8046 (mtt) cc_final: 0.7746 (mtp) REVERT: C 51 THR cc_start: 0.8777 (t) cc_final: 0.8505 (p) REVERT: C 449 PHE cc_start: 0.8215 (t80) cc_final: 0.7393 (t80) REVERT: C 461 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7516 (mt) REVERT: C 466 TYR cc_start: 0.7489 (t80) cc_final: 0.6470 (t80) REVERT: C 477 GLU cc_start: 0.6325 (tp30) cc_final: 0.5813 (pp20) REVERT: C 511 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7142 (mm) REVERT: C 555 PHE cc_start: 0.7685 (p90) cc_final: 0.7337 (p90) REVERT: C 769 LYS cc_start: 0.9148 (tppp) cc_final: 0.8854 (tptm) outliers start: 59 outliers final: 51 residues processed: 226 average time/residue: 0.4378 time to fit residues: 168.0718 Evaluate side-chains 233 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 298 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 73 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 161 optimal weight: 0.0070 chunk 146 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 170 optimal weight: 0.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089340 restraints weight = 67171.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092051 restraints weight = 34437.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093876 restraints weight = 23158.433| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27699 Z= 0.118 Angle : 0.655 15.634 37894 Z= 0.315 Chirality : 0.045 0.374 4529 Planarity : 0.004 0.053 4744 Dihedral : 6.315 59.788 5515 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 2.24 % Allowed : 19.86 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3271 helix: 1.75 (0.20), residues: 731 sheet: 0.01 (0.21), residues: 625 loop : -1.62 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 251 HIS 0.007 0.001 HIS C 648 PHE 0.019 0.001 PHE B 385 TYR 0.019 0.001 TYR C1131 ARG 0.009 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 2.14395 ( 135) link_BETA1-4 : bond 0.00560 ( 47) link_BETA1-4 : angle 1.74533 ( 141) link_ALPHA1-3 : bond 0.01080 ( 1) link_ALPHA1-3 : angle 1.92442 ( 3) hydrogen bonds : bond 0.04546 ( 1002) hydrogen bonds : angle 5.00708 ( 2727) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.16107 ( 84) covalent geometry : bond 0.00265 (27564) covalent geometry : angle 0.63368 (37531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10808.73 seconds wall clock time: 190 minutes 48.30 seconds (11448.30 seconds total)