Starting phenix.real_space_refine on Tue Feb 20 04:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo7_14086/02_2024/7qo7_14086.pdb" } resolution = 3.02 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= 0.016 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 117 5.16 5 C 17092 2.51 5 N 4372 2.21 5 O 5284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26865 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8610 Classifications: {'peptide': 1101} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1044} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "C" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8596 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1041} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.79, per 1000 atoms: 0.55 Number of scatterers: 26865 At special positions: 0 Unit cell: (146.193, 155.797, 194.212, 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 117 16.00 O 5284 8.00 N 4372 7.00 C 17092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG B1301 " - " ASN B 613 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 654 " " NAG B1304 " - " ASN B1071 " " NAG B1305 " - " ASN B 61 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN A 135 " " NAG G 1 " - " ASN A 279 " " NAG H 1 " - " ASN A 706 " " NAG I 1 " - " ASN A1131 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN B 798 " " NAG O 1 " - " ASN B 714 " " NAG P 1 " - " ASN B 706 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN B1095 " " NAG S 1 " - " ASN B 279 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " " NAG V 1 " - " ASN C 706 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1071 " " NAG Z 1 " - " ASN C 279 " Time building additional restraints: 12.28 Conformation dependent library (CDL) restraints added in 5.3 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 47 sheets defined 23.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.955A pdb=" N ASN A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.200A pdb=" N PHE A 152 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.076A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.606A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.968A pdb=" N TYR A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.691A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.616A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 888 " --> pdb=" O PHE A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 4.363A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.548A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.894A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.168A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 618 through 622 removed outlier: 4.033A pdb=" N ILE B 621 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.526A pdb=" N ILE B 739 " --> pdb=" O CYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.251A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.538A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.676A pdb=" N ILE B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.507A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 910 through 937 removed outlier: 6.744A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.644A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.972A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 4.023A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.180A pdb=" N ALA C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.528A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 removed outlier: 4.322A pdb=" N TYR C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 449 " --> pdb=" O TYR C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 449' Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 620 through 624 removed outlier: 4.120A pdb=" N ALA C 623 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.553A pdb=" N CYS C 740 " --> pdb=" O THR C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.514A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.547A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 852 removed outlier: 3.575A pdb=" N GLN C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 937 removed outlier: 4.292A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.649A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.616A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.316A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 190 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 199 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.828A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.718A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 104 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 127 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.785A pdb=" N ARG A 100 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.235A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.975A pdb=" N ARG A 325 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.570A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS A 429 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 510 " --> pdb=" O CYS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.097A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.592A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.904A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 725 removed outlier: 6.904A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.735A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.096A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 221 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 199 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 201 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.081A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.809A pdb=" N PHE B 55 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 268 " --> pdb=" O PHE B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.564A pdb=" N ARG B 234 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 114 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLN B 132 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ASN B 159 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.274A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.931A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.528A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.555A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 572 through 574 Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.105A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.511A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.511A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.752A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.927A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.800A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU C 130 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N CYS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLN C 132 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ASN C 159 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 186 through 192 removed outlier: 3.543A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 199 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.660A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.301A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 507 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.301A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 510 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 429 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 535 through 537 removed outlier: 3.546A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.084A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.537A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.537A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.673A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1117 through 1119 801 hydrogen bonds defined for protein. 2217 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: 10.82 Time building geometry restraints manager: 12.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8423 1.34 - 1.46: 6425 1.46 - 1.58: 12479 1.58 - 1.70: 1 1.70 - 1.82: 147 Bond restraints: 27475 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.603 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.410 1.470 -0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sigma weight residual 1.417 1.473 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.51e+00 ... (remaining 27470 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.49: 737 106.49 - 113.41: 15247 113.41 - 120.33: 9446 120.33 - 127.26: 11710 127.26 - 134.18: 230 Bond angle restraints: 37370 Sorted by residual: angle pdb=" C PHE B 372 " pdb=" N THR B 373 " pdb=" CA THR B 373 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N ILE B 205 " pdb=" CA ILE B 205 " pdb=" C ILE B 205 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.61e+01 angle pdb=" N ILE A 831 " pdb=" CA ILE A 831 " pdb=" C ILE A 831 " ideal model delta sigma weight residual 111.91 108.54 3.37 8.90e-01 1.26e+00 1.44e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 114.39 -3.69 1.22e+00 6.72e-01 9.15e+00 angle pdb=" C ILE B 192 " pdb=" N ASP B 193 " pdb=" CA ASP B 193 " ideal model delta sigma weight residual 122.46 126.68 -4.22 1.41e+00 5.03e-01 8.96e+00 ... (remaining 37365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 16069 24.63 - 49.25: 886 49.25 - 73.88: 145 73.88 - 98.50: 165 98.50 - 123.13: 161 Dihedral angle restraints: 17426 sinusoidal: 7827 harmonic: 9599 Sorted by residual: dihedral pdb=" CB CYS C 837 " pdb=" SG CYS C 837 " pdb=" SG CYS C 848 " pdb=" CB CYS C 848 " ideal model delta sinusoidal sigma weight residual 93.00 -178.45 -88.55 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -22.41 -63.59 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 17423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4374 0.123 - 0.247: 57 0.247 - 0.370: 21 0.370 - 0.494: 0 0.494 - 0.617: 1 Chirality restraints: 4453 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 706 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 135 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 654 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4450 not shown) Planarity restraints: 4755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 369 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 370 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " 0.013 2.00e-02 2.50e+03 1.41e-02 4.97e+00 pdb=" CG TRP B 64 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 630 " 0.015 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP A 630 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 630 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 630 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 630 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 630 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 630 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 630 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 630 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 630 " 0.005 2.00e-02 2.50e+03 ... (remaining 4752 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 853 2.71 - 3.26: 26221 3.26 - 3.81: 40534 3.81 - 4.35: 49159 4.35 - 4.90: 84367 Nonbonded interactions: 201134 Sorted by model distance: nonbonded pdb=" OG1 THR B1113 " pdb=" OD1 ASP B1115 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR A 753 " pdb=" OD1 ASP A 991 " model vdw 2.173 2.440 nonbonded pdb=" OH TYR B 377 " pdb=" O PRO B 409 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR A 89 " pdb=" OE1 GLU A 186 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR A 106 " pdb=" O ASN A 231 " model vdw 2.222 2.440 ... (remaining 201129 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 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 1304)) selection = (chain 'B' and (resid 19 through 441 or resid 444 through 1144 or resid 1301 thr \ ough 1304)) selection = (chain 'C' and (resid 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 10.370 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 74.440 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.180 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: 92.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.004 0.084 27475 Z= 0.238 Angle : 0.636 8.380 37370 Z= 0.297 Chirality : 0.050 0.617 4453 Planarity : 0.004 0.056 4718 Dihedral : 21.438 123.130 11126 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3261 helix: 1.72 (0.22), residues: 682 sheet: -0.01 (0.24), residues: 508 loop : -1.38 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 64 HIS 0.003 0.000 HIS C 242 PHE 0.029 0.001 PHE C 65 TYR 0.026 0.001 TYR A 901 ARG 0.005 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 2.930 Fit side-chains revert: symmetry clash REVERT: A 899 MET cc_start: 0.7989 (tpp) cc_final: 0.7762 (tpt) REVERT: B 749 LEU cc_start: 0.8980 (mp) cc_final: 0.8505 (tt) REVERT: C 262 TYR cc_start: 0.7118 (p90) cc_final: 0.6734 (p90) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.3423 time to fit residues: 103.9889 Evaluate side-chains 128 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 0.0000 chunk 257 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27475 Z= 0.248 Angle : 0.641 9.829 37370 Z= 0.304 Chirality : 0.050 0.581 4453 Planarity : 0.004 0.065 4718 Dihedral : 18.040 111.245 5199 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 0.56 % Allowed : 5.80 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3261 helix: 1.67 (0.21), residues: 688 sheet: -0.05 (0.23), residues: 498 loop : -1.54 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 630 HIS 0.005 0.001 HIS C 202 PHE 0.021 0.001 PHE B 903 TYR 0.020 0.001 TYR A1064 ARG 0.003 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 3.047 Fit side-chains revert: symmetry clash REVERT: B 749 LEU cc_start: 0.9004 (mp) cc_final: 0.8598 (tt) REVERT: C 262 TYR cc_start: 0.7067 (p90) cc_final: 0.6727 (p90) REVERT: C 1007 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7941 (mp10) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.3366 time to fit residues: 88.0867 Evaluate side-chains 132 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1007 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 7.9990 chunk 92 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 265 optimal weight: 30.0000 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27475 Z= 0.230 Angle : 0.603 11.328 37370 Z= 0.289 Chirality : 0.048 0.607 4453 Planarity : 0.004 0.071 4718 Dihedral : 14.099 111.433 5199 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.62 % Favored : 93.13 % Rotamer: Outliers : 0.98 % Allowed : 8.69 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3261 helix: 1.75 (0.21), residues: 675 sheet: -0.18 (0.22), residues: 526 loop : -1.57 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 630 HIS 0.004 0.001 HIS B 242 PHE 0.023 0.001 PHE A 217 TYR 0.017 0.001 TYR B1064 ARG 0.003 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 2.937 Fit side-chains revert: symmetry clash REVERT: A 977 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8864 (tt) REVERT: B 749 LEU cc_start: 0.9035 (mp) cc_final: 0.8622 (tt) outliers start: 28 outliers final: 18 residues processed: 164 average time/residue: 0.3462 time to fit residues: 96.1897 Evaluate side-chains 146 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 142 optimal weight: 0.1980 chunk 200 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27475 Z= 0.269 Angle : 0.598 11.124 37370 Z= 0.292 Chirality : 0.048 0.652 4453 Planarity : 0.004 0.073 4718 Dihedral : 12.481 114.024 5199 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 1.12 % Allowed : 11.10 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3261 helix: 1.68 (0.21), residues: 678 sheet: -0.31 (0.23), residues: 497 loop : -1.63 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 630 HIS 0.004 0.001 HIS A1061 PHE 0.022 0.001 PHE C 104 TYR 0.017 0.001 TYR A1064 ARG 0.004 0.000 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 3.238 Fit side-chains REVERT: B 749 LEU cc_start: 0.9071 (mp) cc_final: 0.8673 (tt) REVERT: C 494 PHE cc_start: 0.1976 (OUTLIER) cc_final: 0.1054 (t80) REVERT: C 1007 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7747 (mp10) outliers start: 32 outliers final: 20 residues processed: 164 average time/residue: 0.3395 time to fit residues: 94.1588 Evaluate side-chains 149 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 219 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B 989 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27475 Z= 0.405 Angle : 0.667 10.155 37370 Z= 0.330 Chirality : 0.050 0.746 4453 Planarity : 0.005 0.076 4718 Dihedral : 11.822 116.090 5199 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 1.89 % Allowed : 12.78 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3261 helix: 1.43 (0.21), residues: 675 sheet: -0.50 (0.23), residues: 512 loop : -1.85 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 630 HIS 0.010 0.001 HIS A 242 PHE 0.025 0.002 PHE A 217 TYR 0.020 0.002 TYR C 89 ARG 0.007 0.001 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 2.955 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.1184 (OUTLIER) cc_final: 0.0971 (mt) REVERT: B 140 ASP cc_start: 0.5027 (OUTLIER) cc_final: 0.4074 (m-30) REVERT: B 616 GLU cc_start: 0.8068 (mp0) cc_final: 0.7809 (mp0) REVERT: B 749 LEU cc_start: 0.9079 (mp) cc_final: 0.8719 (tt) REVERT: B 982 ASP cc_start: 0.7861 (p0) cc_final: 0.7172 (p0) REVERT: C 494 PHE cc_start: 0.1928 (OUTLIER) cc_final: 0.1064 (t80) outliers start: 54 outliers final: 35 residues processed: 179 average time/residue: 0.3450 time to fit residues: 106.5063 Evaluate side-chains 169 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 263 optimal weight: 0.0470 chunk 146 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 314 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27475 Z= 0.168 Angle : 0.577 10.656 37370 Z= 0.279 Chirality : 0.046 0.621 4453 Planarity : 0.004 0.076 4718 Dihedral : 10.957 117.499 5199 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.13 % Rotamer: Outliers : 1.08 % Allowed : 14.70 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3261 helix: 1.74 (0.21), residues: 672 sheet: -0.35 (0.23), residues: 488 loop : -1.73 (0.12), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 630 HIS 0.003 0.001 HIS A 202 PHE 0.017 0.001 PHE A 217 TYR 0.017 0.001 TYR B1064 ARG 0.004 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 238 LEU cc_start: 0.7949 (mt) cc_final: 0.7407 (mm) REVERT: B 362 TYR cc_start: 0.7817 (m-80) cc_final: 0.7257 (m-80) REVERT: B 616 GLU cc_start: 0.8055 (mp0) cc_final: 0.7785 (mp0) REVERT: B 749 LEU cc_start: 0.9090 (mp) cc_final: 0.8844 (tt) REVERT: C 494 PHE cc_start: 0.1946 (OUTLIER) cc_final: 0.1075 (t80) REVERT: C 749 LEU cc_start: 0.8675 (mp) cc_final: 0.8331 (tp) REVERT: C 899 MET cc_start: 0.8321 (tpt) cc_final: 0.7774 (tpt) REVERT: C 980 ARG cc_start: 0.7532 (mtm110) cc_final: 0.6526 (mpt180) REVERT: C 1007 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7663 (mp10) outliers start: 31 outliers final: 20 residues processed: 176 average time/residue: 0.3426 time to fit residues: 102.1034 Evaluate side-chains 160 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 316 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27475 Z= 0.302 Angle : 0.615 10.066 37370 Z= 0.302 Chirality : 0.048 0.702 4453 Planarity : 0.004 0.077 4718 Dihedral : 10.525 119.953 5199 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.79 % Favored : 91.93 % Rotamer: Outliers : 1.26 % Allowed : 15.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3261 helix: 1.60 (0.21), residues: 675 sheet: -0.43 (0.23), residues: 488 loop : -1.82 (0.12), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.019 0.001 PHE A 217 TYR 0.018 0.001 TYR B 89 ARG 0.005 0.000 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (mm) REVERT: B 140 ASP cc_start: 0.4863 (OUTLIER) cc_final: 0.3870 (m-30) REVERT: B 616 GLU cc_start: 0.8061 (mp0) cc_final: 0.7776 (mp0) REVERT: B 749 LEU cc_start: 0.9176 (mp) cc_final: 0.8872 (tt) REVERT: C 494 PHE cc_start: 0.1948 (OUTLIER) cc_final: 0.1069 (t80) REVERT: C 749 LEU cc_start: 0.8847 (mp) cc_final: 0.8487 (tp) outliers start: 36 outliers final: 28 residues processed: 163 average time/residue: 0.3373 time to fit residues: 94.0223 Evaluate side-chains 160 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS B 191 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27475 Z= 0.227 Angle : 0.589 9.943 37370 Z= 0.289 Chirality : 0.047 0.663 4453 Planarity : 0.004 0.078 4718 Dihedral : 10.209 120.706 5199 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.13 % Rotamer: Outliers : 1.61 % Allowed : 15.12 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3261 helix: 1.71 (0.21), residues: 671 sheet: -0.47 (0.23), residues: 502 loop : -1.79 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 630 HIS 0.003 0.001 HIS A1061 PHE 0.029 0.001 PHE A 104 TYR 0.017 0.001 TYR B1064 ARG 0.006 0.000 ARG C 980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 140 ASP cc_start: 0.4885 (OUTLIER) cc_final: 0.3936 (m-30) REVERT: B 616 GLU cc_start: 0.8051 (mp0) cc_final: 0.7760 (mp0) REVERT: B 749 LEU cc_start: 0.9199 (mp) cc_final: 0.8924 (tt) REVERT: C 494 PHE cc_start: 0.2193 (OUTLIER) cc_final: 0.1235 (t80) REVERT: C 749 LEU cc_start: 0.8813 (mp) cc_final: 0.8492 (tp) outliers start: 46 outliers final: 31 residues processed: 176 average time/residue: 0.3333 time to fit residues: 100.6810 Evaluate side-chains 168 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.5980 chunk 302 optimal weight: 0.5980 chunk 276 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 266 optimal weight: 50.0000 chunk 278 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27475 Z= 0.214 Angle : 0.587 9.922 37370 Z= 0.286 Chirality : 0.047 0.656 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.995 120.091 5199 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.18 % Favored : 92.49 % Rotamer: Outliers : 1.22 % Allowed : 15.78 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.14), residues: 3261 helix: 1.71 (0.21), residues: 672 sheet: -0.40 (0.23), residues: 495 loop : -1.76 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 630 HIS 0.003 0.001 HIS A1061 PHE 0.019 0.001 PHE C 163 TYR 0.018 0.001 TYR C 165 ARG 0.006 0.000 ARG C 980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 616 GLU cc_start: 0.8071 (mp0) cc_final: 0.7796 (mp0) REVERT: B 749 LEU cc_start: 0.9195 (mp) cc_final: 0.8931 (tt) REVERT: C 326 PHE cc_start: 0.7370 (t80) cc_final: 0.7064 (t80) REVERT: C 494 PHE cc_start: 0.2170 (OUTLIER) cc_final: 0.1249 (t80) REVERT: C 749 LEU cc_start: 0.8784 (mp) cc_final: 0.8476 (tp) outliers start: 35 outliers final: 33 residues processed: 162 average time/residue: 0.3415 time to fit residues: 94.3905 Evaluate side-chains 170 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 216 optimal weight: 0.0270 chunk 326 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 260 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27475 Z= 0.209 Angle : 0.584 9.844 37370 Z= 0.286 Chirality : 0.046 0.654 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.671 119.644 5199 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 1.22 % Allowed : 15.92 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3261 helix: 1.73 (0.21), residues: 673 sheet: -0.33 (0.23), residues: 502 loop : -1.77 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 630 HIS 0.003 0.001 HIS A1061 PHE 0.035 0.001 PHE A 104 TYR 0.017 0.001 TYR B1064 ARG 0.006 0.000 ARG C 980 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4064 (m-30) REVERT: B 616 GLU cc_start: 0.8095 (mp0) cc_final: 0.7820 (mp0) REVERT: B 749 LEU cc_start: 0.9169 (mp) cc_final: 0.8964 (tt) REVERT: C 494 PHE cc_start: 0.2168 (OUTLIER) cc_final: 0.1244 (t80) REVERT: C 749 LEU cc_start: 0.8755 (mp) cc_final: 0.8498 (tp) REVERT: C 1007 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7757 (mp10) outliers start: 35 outliers final: 31 residues processed: 163 average time/residue: 0.3336 time to fit residues: 92.8187 Evaluate side-chains 170 residues out of total 2873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 978 PHE Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 239 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 260 optimal weight: 50.0000 chunk 109 optimal weight: 0.0050 chunk 267 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.155337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.091191 restraints weight = 55088.790| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.59 r_work: 0.3195 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27475 Z= 0.141 Angle : 0.560 9.769 37370 Z= 0.272 Chirality : 0.045 0.585 4453 Planarity : 0.004 0.078 4718 Dihedral : 9.238 119.134 5199 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.56 % Favored : 93.16 % Rotamer: Outliers : 0.80 % Allowed : 16.55 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3261 helix: 1.84 (0.22), residues: 675 sheet: -0.20 (0.23), residues: 520 loop : -1.66 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 630 HIS 0.003 0.000 HIS A 202 PHE 0.038 0.001 PHE C 163 TYR 0.029 0.001 TYR C 263 ARG 0.006 0.000 ARG C 980 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5118.75 seconds wall clock time: 94 minutes 45.33 seconds (5685.33 seconds total)