Starting phenix.real_space_refine on Tue Feb 20 14:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0d_30531/02_2024/7d0d_30531.pdb" } resolution = 3.8 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= 0.000 sd= 0.004 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 121 5.16 5 C 17873 2.51 5 N 4562 2.21 5 O 5540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28096 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "C" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "F" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.70, per 1000 atoms: 0.52 Number of scatterers: 28096 At special positions: 0 Unit cell: (136.962, 169.572, 221.748, 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 121 16.00 O 5540 8.00 N 4562 7.00 C 17873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.64 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.78 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN C 331 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C1074 " Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 4.7 seconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6500 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 60 sheets defined 21.0% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.641A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 103 through 106 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.995A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 291 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.878A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.914A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.810A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.732A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.307A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 69 through 74 Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS L 113 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 13 " --> pdb=" O LYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.881A pdb=" N ILE L 81 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.595A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'G' and resid 59 through 61 removed outlier: 6.307A pdb=" N TRP G 38 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU G 52 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL G 36 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR G 54 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL G 34 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 69 through 74 Processing sheet with id=AE8, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'F' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU F 11 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS F 113 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL F 13 " --> pdb=" O LYS F 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.881A pdb=" N ILE F 81 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.596A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF6, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.732A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.678A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2688 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: 12.73 Time building geometry restraints manager: 11.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8661 1.34 - 1.46: 7456 1.46 - 1.59: 12440 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 28711 Sorted by residual: bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.59e-02 3.96e+03 1.75e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO F 101 " pdb=" CD PRO F 101 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO L 101 " pdb=" CD PRO L 101 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 28706 not shown) Histogram of bond angle deviations from ideal: 97.55 - 105.80: 590 105.80 - 114.06: 16828 114.06 - 122.31: 16754 122.31 - 130.56: 4804 130.56 - 138.82: 84 Bond angle restraints: 39060 Sorted by residual: angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N GLU A 156 " pdb=" CA GLU A 156 " pdb=" C GLU A 156 " ideal model delta sigma weight residual 108.45 115.82 -7.37 1.26e+00 6.30e-01 3.42e+01 angle pdb=" C THR A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 119.78 114.06 5.72 1.03e+00 9.43e-01 3.08e+01 angle pdb=" C LEU C 212 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 123.08 117.61 5.47 1.01e+00 9.80e-01 2.93e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 122.56 115.26 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 39055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15482 17.91 - 35.82: 1760 35.82 - 53.73: 529 53.73 - 71.64: 173 71.64 - 89.55: 56 Dihedral angle restraints: 18000 sinusoidal: 7907 harmonic: 10093 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.60 73.40 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 4641 0.328 - 0.656: 3 0.656 - 0.984: 4 0.984 - 1.312: 0 1.312 - 1.640: 1 Chirality restraints: 4649 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.98e+01 ... (remaining 4646 not shown) Planarity restraints: 4980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.133 2.00e-02 2.50e+03 1.86e-01 4.33e+02 pdb=" CG ASN A 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.327 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 527 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.022 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" CG ASN A1134 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.034 2.00e-02 2.50e+03 ... (remaining 4977 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 343 2.57 - 3.15: 22049 3.15 - 3.73: 41810 3.73 - 4.32: 61132 4.32 - 4.90: 100994 Nonbonded interactions: 226328 Sorted by model distance: nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 2.520 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 2.520 nonbonded pdb=" O SER H 110 " pdb=" CD1 TRP H 111 " model vdw 2.020 3.260 nonbonded pdb=" O SER G 110 " pdb=" CD1 TRP G 111 " model vdw 2.020 3.260 nonbonded pdb=" O SER G 110 " pdb=" CG TRP G 111 " model vdw 2.033 3.260 ... (remaining 226323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1146 or resid 1401 through \ 1408)) selection = (chain 'B' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 11 \ 46 or resid 1401 through 1408)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.650 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 74.260 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.011 0.118 28711 Z= 0.710 Angle : 1.030 13.818 39060 Z= 0.586 Chirality : 0.071 1.640 4649 Planarity : 0.007 0.091 4932 Dihedral : 17.646 89.551 11374 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.59 % Favored : 89.29 % Rotamer: Outliers : 11.01 % Allowed : 18.07 % Favored : 70.93 % 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: -3.87 (0.12), residues: 3400 helix: -2.12 (0.17), residues: 647 sheet: -2.15 (0.16), residues: 847 loop : -3.02 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS B1048 PHE 0.035 0.003 PHE G 24 TYR 0.026 0.003 TYR C1067 ARG 0.009 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 486 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.6431 (p) REVERT: A 587 ILE cc_start: 0.9124 (mt) cc_final: 0.8878 (mt) REVERT: A 975 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8463 (p) REVERT: A 1104 VAL cc_start: 0.9511 (OUTLIER) cc_final: 0.9308 (t) REVERT: C 52 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: C 317 ASN cc_start: 0.8275 (m110) cc_final: 0.7946 (t0) REVERT: C 409 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.4895 (tp40) REVERT: C 869 MET cc_start: 0.7832 (mtt) cc_final: 0.7574 (mtt) REVERT: C 1050 MET cc_start: 0.8145 (ptm) cc_final: 0.7863 (ptm) REVERT: L 66 ASP cc_start: 0.6990 (m-30) cc_final: 0.6586 (p0) REVERT: F 97 TYR cc_start: 0.0242 (t80) cc_final: -0.0200 (t80) REVERT: B 81 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7993 (m110) REVERT: B 459 SER cc_start: 0.1990 (OUTLIER) cc_final: 0.1644 (p) REVERT: B 692 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 1051 SER cc_start: 0.9365 (m) cc_final: 0.8868 (p) REVERT: B 1077 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8861 (m) outliers start: 335 outliers final: 70 residues processed: 753 average time/residue: 0.3836 time to fit residues: 453.9471 Evaluate side-chains 263 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 184 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 269 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 312 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 125 ASN A 188 ASN A 207 HIS A 211 ASN A 280 ASN A 321 GLN A 394 ASN A 422 ASN A 606 ASN A 641 ASN A 690 GLN A 703 ASN A 751 ASN A 901 GLN A 914 ASN A 926 GLN A 992 GLN A1071 GLN A1101 HIS C 66 HIS C 115 GLN C 134 GLN C 188 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 540 ASN C 563 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN C 914 ASN C 919 ASN C 920 GLN C 926 GLN C 935 GLN C 954 GLN C 992 GLN C1054 GLN H 41 GLN H 119 GLN L 6 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 HIS G 41 GLN F 6 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 HIS B 49 HIS B 66 HIS B 115 GLN B 134 GLN B 137 ASN B 164 ASN B 239 GLN B 354 ASN B 422 ASN B 440 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 644 GLN B 690 GLN B 703 ASN B 764 ASN B 856 ASN B 901 GLN B 907 ASN B 914 ASN B 919 ASN B 926 GLN B 955 ASN B 969 ASN B 992 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28711 Z= 0.262 Angle : 0.777 11.346 39060 Z= 0.389 Chirality : 0.050 0.368 4649 Planarity : 0.005 0.058 4932 Dihedral : 9.803 88.157 5303 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.29 % Favored : 92.50 % Rotamer: Outliers : 5.62 % Allowed : 20.66 % Favored : 73.72 % 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: -2.58 (0.13), residues: 3400 helix: 0.05 (0.20), residues: 650 sheet: -1.55 (0.16), residues: 830 loop : -2.51 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 117 HIS 0.007 0.001 HIS C 519 PHE 0.030 0.002 PHE H 114 TYR 0.026 0.002 TYR B 453 ARG 0.009 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 207 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6389 (mttt) REVERT: A 587 ILE cc_start: 0.9150 (mt) cc_final: 0.8847 (mt) REVERT: C 87 ASN cc_start: 0.4618 (OUTLIER) cc_final: 0.3200 (m-40) REVERT: C 88 ASP cc_start: 0.6814 (m-30) cc_final: 0.6576 (m-30) REVERT: C 214 ARG cc_start: 0.0117 (OUTLIER) cc_final: -0.0353 (ttt180) REVERT: C 811 LYS cc_start: 0.7219 (mttp) cc_final: 0.6402 (tptp) REVERT: C 1050 MET cc_start: 0.7764 (ptm) cc_final: 0.7502 (ptm) REVERT: C 1136 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (p) REVERT: H 100 SER cc_start: -0.0501 (OUTLIER) cc_final: -0.1025 (t) REVERT: H 114 PHE cc_start: 0.2598 (m-10) cc_final: 0.2381 (m-10) REVERT: L 66 ASP cc_start: 0.7428 (m-30) cc_final: 0.7125 (p0) REVERT: B 285 ILE cc_start: 0.8991 (mt) cc_final: 0.8769 (mt) REVERT: B 540 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7465 (m-40) REVERT: B 1029 MET cc_start: 0.8465 (tpp) cc_final: 0.8034 (tpp) outliers start: 171 outliers final: 92 residues processed: 364 average time/residue: 0.3519 time to fit residues: 216.0240 Evaluate side-chains 237 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 139 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 394 ASN A 414 GLN A 450 ASN A 498 GLN A 501 ASN A 542 ASN A 926 GLN C 66 HIS C 422 ASN C 493 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 913 GLN C1135 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1011 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28711 Z= 0.336 Angle : 0.733 10.979 39060 Z= 0.365 Chirality : 0.049 0.285 4649 Planarity : 0.005 0.060 4932 Dihedral : 8.470 66.279 5242 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.26 % Favored : 92.56 % Rotamer: Outliers : 5.16 % Allowed : 21.88 % Favored : 72.96 % 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: -2.07 (0.13), residues: 3400 helix: 0.76 (0.21), residues: 662 sheet: -1.44 (0.16), residues: 864 loop : -2.20 (0.12), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 111 HIS 0.008 0.001 HIS F 102 PHE 0.033 0.002 PHE A 464 TYR 0.022 0.002 TYR B 365 ARG 0.005 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 147 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8863 (p) REVERT: A 301 CYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6337 (m) REVERT: A 587 ILE cc_start: 0.9156 (mt) cc_final: 0.8831 (mt) REVERT: C 214 ARG cc_start: 0.0511 (OUTLIER) cc_final: -0.0444 (ttt180) REVERT: C 811 LYS cc_start: 0.7295 (mttp) cc_final: 0.6578 (tptp) REVERT: C 1050 MET cc_start: 0.7631 (ptm) cc_final: 0.7410 (ptm) REVERT: C 1136 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8225 (p) REVERT: H 49 TRP cc_start: 0.3090 (t60) cc_final: 0.1769 (t60) REVERT: H 111 TRP cc_start: 0.5848 (p90) cc_final: 0.5146 (p90) REVERT: L 66 ASP cc_start: 0.7581 (m-30) cc_final: 0.7277 (p0) outliers start: 157 outliers final: 96 residues processed: 291 average time/residue: 0.3288 time to fit residues: 164.8514 Evaluate side-chains 220 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 120 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 314 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 207 HIS A 394 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1002 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 460 ASN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 43 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B1106 GLN B1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28711 Z= 0.243 Angle : 0.664 11.175 39060 Z= 0.328 Chirality : 0.047 0.251 4649 Planarity : 0.004 0.058 4932 Dihedral : 7.844 59.579 5225 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.74 % Favored : 93.09 % Rotamer: Outliers : 5.12 % Allowed : 22.21 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.76 (0.14), residues: 3400 helix: 1.05 (0.21), residues: 672 sheet: -1.18 (0.17), residues: 822 loop : -2.07 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 111 HIS 0.004 0.001 HIS F 102 PHE 0.026 0.002 PHE A 456 TYR 0.019 0.001 TYR F 97 ARG 0.019 0.001 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 138 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7475 (mttm) REVERT: A 287 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: A 587 ILE cc_start: 0.9115 (mt) cc_final: 0.8772 (mt) REVERT: C 214 ARG cc_start: 0.0232 (OUTLIER) cc_final: -0.0717 (ttt180) REVERT: C 811 LYS cc_start: 0.7069 (mttp) cc_final: 0.6469 (tptp) REVERT: C 912 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8496 (p) REVERT: H 39 ILE cc_start: 0.2936 (OUTLIER) cc_final: 0.2153 (mt) REVERT: L 66 ASP cc_start: 0.7645 (m-30) cc_final: 0.7360 (p0) REVERT: L 108 THR cc_start: 0.0168 (OUTLIER) cc_final: -0.0080 (t) REVERT: F 34 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7234 (t0) outliers start: 156 outliers final: 100 residues processed: 284 average time/residue: 0.3497 time to fit residues: 168.0776 Evaluate side-chains 227 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 120 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 4 optimal weight: 0.0030 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 6.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 188 ASN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 926 GLN C 935 GLN H 41 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 658 ASN B 907 ASN B1088 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 28711 Z= 0.522 Angle : 0.837 11.510 39060 Z= 0.414 Chirality : 0.052 0.309 4649 Planarity : 0.005 0.056 4932 Dihedral : 8.403 59.883 5220 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.74 % Favored : 91.06 % Rotamer: Outliers : 5.81 % Allowed : 22.21 % Favored : 71.98 % 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: -1.92 (0.14), residues: 3400 helix: 0.74 (0.21), residues: 676 sheet: -1.10 (0.17), residues: 841 loop : -2.20 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP H 111 HIS 0.008 0.002 HIS C 49 PHE 0.030 0.003 PHE C 135 TYR 0.022 0.002 TYR B 365 ARG 0.007 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 126 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: A 429 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5591 (t80) REVERT: A 587 ILE cc_start: 0.9204 (mt) cc_final: 0.8877 (mt) REVERT: C 869 MET cc_start: 0.8184 (mtt) cc_final: 0.7894 (mtt) REVERT: C 912 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 1050 MET cc_start: 0.7693 (ptm) cc_final: 0.7410 (ptp) REVERT: H 39 ILE cc_start: 0.2697 (OUTLIER) cc_final: 0.2378 (mt) REVERT: H 111 TRP cc_start: 0.5097 (p90) cc_final: 0.4838 (p90) REVERT: H 114 PHE cc_start: 0.2169 (m-10) cc_final: 0.1919 (m-10) REVERT: L 66 ASP cc_start: 0.7786 (m-30) cc_final: 0.7485 (p0) REVERT: B 567 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6940 (mmm-85) outliers start: 177 outliers final: 131 residues processed: 291 average time/residue: 0.3300 time to fit residues: 164.4422 Evaluate side-chains 247 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 111 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 332 optimal weight: 0.7980 chunk 276 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN C 30 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 690 GLN C 804 GLN C 935 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 501 ASN B1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28711 Z= 0.165 Angle : 0.639 11.523 39060 Z= 0.314 Chirality : 0.047 0.253 4649 Planarity : 0.004 0.056 4932 Dihedral : 7.591 59.117 5220 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.65 % Rotamer: Outliers : 3.81 % Allowed : 23.85 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.45 (0.14), residues: 3400 helix: 1.30 (0.21), residues: 678 sheet: -0.83 (0.17), residues: 830 loop : -1.95 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 111 HIS 0.005 0.001 HIS B 207 PHE 0.021 0.001 PHE A 43 TYR 0.022 0.001 TYR F 97 ARG 0.006 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 132 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: A 332 ILE cc_start: 0.5865 (OUTLIER) cc_final: 0.5503 (mt) REVERT: A 429 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.5603 (t80) REVERT: A 464 PHE cc_start: 0.6486 (m-80) cc_final: 0.6225 (m-80) REVERT: A 587 ILE cc_start: 0.9118 (mt) cc_final: 0.8749 (mt) REVERT: C 214 ARG cc_start: 0.0216 (OUTLIER) cc_final: -0.1006 (mtt180) REVERT: H 114 PHE cc_start: 0.2182 (OUTLIER) cc_final: 0.1902 (m-10) REVERT: L 66 ASP cc_start: 0.7684 (m-30) cc_final: 0.7460 (p0) REVERT: B 517 LEU cc_start: 0.4417 (OUTLIER) cc_final: 0.3603 (mt) outliers start: 116 outliers final: 82 residues processed: 239 average time/residue: 0.3709 time to fit residues: 155.0447 Evaluate side-chains 203 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 115 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 331 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28711 Z= 0.403 Angle : 0.725 11.550 39060 Z= 0.356 Chirality : 0.049 0.272 4649 Planarity : 0.004 0.058 4932 Dihedral : 7.751 59.540 5213 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.62 % Rotamer: Outliers : 4.63 % Allowed : 23.52 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.14), residues: 3400 helix: 1.20 (0.21), residues: 666 sheet: -0.87 (0.17), residues: 835 loop : -1.99 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 111 HIS 0.011 0.001 HIS H 99 PHE 0.020 0.002 PHE B 86 TYR 0.022 0.002 TYR C 160 ARG 0.005 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 116 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5507 (mt) REVERT: A 429 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5775 (t80) REVERT: A 587 ILE cc_start: 0.9212 (mt) cc_final: 0.8878 (mt) REVERT: C 1050 MET cc_start: 0.7910 (ptp) cc_final: 0.7642 (ptm) REVERT: L 66 ASP cc_start: 0.7785 (m-30) cc_final: 0.7557 (p0) outliers start: 141 outliers final: 106 residues processed: 247 average time/residue: 0.3322 time to fit residues: 142.4233 Evaluate side-chains 218 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 110 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 210 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 260 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28711 Z= 0.160 Angle : 0.622 11.516 39060 Z= 0.304 Chirality : 0.046 0.268 4649 Planarity : 0.004 0.058 4932 Dihedral : 7.181 59.218 5209 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 3.61 % Allowed : 24.24 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.23 (0.14), residues: 3400 helix: 1.49 (0.21), residues: 668 sheet: -0.66 (0.17), residues: 872 loop : -1.83 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP H 111 HIS 0.005 0.001 HIS B 207 PHE 0.020 0.001 PHE B 497 TYR 0.020 0.001 TYR B 495 ARG 0.004 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 123 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5620 (t80) REVERT: A 464 PHE cc_start: 0.6484 (m-80) cc_final: 0.6242 (m-80) REVERT: A 587 ILE cc_start: 0.9176 (mt) cc_final: 0.8854 (mt) REVERT: B 517 LEU cc_start: 0.4081 (OUTLIER) cc_final: 0.3444 (mt) REVERT: B 1051 SER cc_start: 0.9222 (m) cc_final: 0.8976 (p) outliers start: 110 outliers final: 80 residues processed: 227 average time/residue: 0.3640 time to fit residues: 140.3067 Evaluate side-chains 200 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 118 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 0.0870 chunk 317 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 308 optimal weight: 0.0270 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 307 optimal weight: 0.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28711 Z= 0.152 Angle : 0.604 11.395 39060 Z= 0.294 Chirality : 0.046 0.254 4649 Planarity : 0.004 0.055 4932 Dihedral : 6.808 59.167 5204 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 2.89 % Allowed : 24.67 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3400 helix: 1.64 (0.21), residues: 668 sheet: -0.59 (0.17), residues: 889 loop : -1.74 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 111 HIS 0.005 0.001 HIS F 102 PHE 0.020 0.001 PHE C 86 TYR 0.037 0.001 TYR B 495 ARG 0.009 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 136 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8483 (pt) cc_final: 0.8257 (tp) REVERT: A 429 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5737 (t80) REVERT: A 464 PHE cc_start: 0.6333 (m-80) cc_final: 0.6034 (m-80) REVERT: A 508 TYR cc_start: 0.6619 (m-80) cc_final: 0.6214 (m-10) REVERT: A 587 ILE cc_start: 0.9189 (mt) cc_final: 0.8848 (mt) REVERT: C 214 ARG cc_start: 0.0795 (OUTLIER) cc_final: -0.0657 (mmt90) REVERT: H 114 PHE cc_start: 0.2105 (m-10) cc_final: 0.1874 (m-10) REVERT: B 517 LEU cc_start: 0.4160 (OUTLIER) cc_final: 0.3601 (mt) REVERT: B 1051 SER cc_start: 0.9181 (m) cc_final: 0.8981 (p) outliers start: 88 outliers final: 73 residues processed: 218 average time/residue: 0.3453 time to fit residues: 127.7472 Evaluate side-chains 195 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 119 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.6980 chunk 326 optimal weight: 0.9990 chunk 199 optimal weight: 40.0000 chunk 154 optimal weight: 3.9990 chunk 227 optimal weight: 40.0000 chunk 342 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN B 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28711 Z= 0.303 Angle : 0.665 11.501 39060 Z= 0.326 Chirality : 0.048 0.256 4649 Planarity : 0.004 0.057 4932 Dihedral : 7.022 59.421 5196 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.71 % Favored : 92.21 % Rotamer: Outliers : 2.99 % Allowed : 24.77 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.15 (0.14), residues: 3400 helix: 1.53 (0.21), residues: 668 sheet: -0.51 (0.17), residues: 854 loop : -1.82 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP H 111 HIS 0.006 0.001 HIS F 102 PHE 0.024 0.002 PHE C 86 TYR 0.032 0.001 TYR F 97 ARG 0.006 0.001 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 115 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 587 ILE cc_start: 0.9246 (mt) cc_final: 0.8951 (mt) REVERT: C 214 ARG cc_start: 0.0698 (OUTLIER) cc_final: -0.0958 (mmt90) REVERT: C 231 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (mm) REVERT: H 13 LYS cc_start: 0.4620 (mmtm) cc_final: 0.4339 (mtmm) REVERT: B 517 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3288 (mt) outliers start: 91 outliers final: 82 residues processed: 200 average time/residue: 0.3365 time to fit residues: 118.6839 Evaluate side-chains 193 residues out of total 3044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 107 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 280 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 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 = 0.3763 r_free = 0.3763 target = 0.103213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066068 restraints weight = 87484.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.067370 restraints weight = 59196.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067719 restraints weight = 37487.420| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28711 Z= 0.418 Angle : 0.727 11.663 39060 Z= 0.358 Chirality : 0.049 0.268 4649 Planarity : 0.005 0.063 4932 Dihedral : 7.416 59.466 5196 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.15 % Allowed : 25.03 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.32 (0.14), residues: 3400 helix: 1.31 (0.21), residues: 666 sheet: -0.66 (0.17), residues: 868 loop : -1.87 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP H 111 HIS 0.007 0.001 HIS C 49 PHE 0.021 0.002 PHE B 86 TYR 0.041 0.002 TYR B 495 ARG 0.006 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.20 seconds wall clock time: 90 minutes 9.03 seconds (5409.03 seconds total)