Starting phenix.real_space_refine on Wed Feb 21 07:33:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyp_30503/02_2024/7cyp_30503.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 128 5.16 5 C 19027 2.51 5 N 4943 2.21 5 O 5881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 48": "NH1" <-> "NH2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 100": "NH1" <-> "NH2" 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: 29979 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7988 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7988 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7987 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 19.35, per 1000 atoms: 0.65 Number of scatterers: 29979 At special positions: 0 Unit cell: (159.6, 173.25, 222.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 5881 8.00 N 4943 7.00 C 19027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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=2, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 5.8 seconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 72 sheets defined 19.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.563A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.749A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.344A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.864A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.795A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.688A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.813A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.646A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.990A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 905 removed outlier: 3.956A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 915 through 940 removed outlier: 5.153A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.562A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.563A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.750A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.343A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.864A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 755 removed outlier: 3.795A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.688A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.813A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.646A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 889 removed outlier: 3.990A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 905 removed outlier: 3.956A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 940 removed outlier: 5.153A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.561A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.106A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 295 through 304 removed outlier: 4.051A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.549A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.556A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.915A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.560A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.930A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.724A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.648A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.581A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.228A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.601A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.725A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.945A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.506A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.824A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.144A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.856A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.600A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.725A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.945A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.506A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.824A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.144A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.638A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.826A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.650A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 93 through 95 removed outlier: 4.238A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.853A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 7.004A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 313 through 317 removed outlier: 5.769A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.574A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.735A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 401 through 403 removed outlier: 4.091A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.189A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 721 through 728 removed outlier: 7.076A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.078A pdb=" N VAL D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU D 10 " --> pdb=" O GLU D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.119A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AG4, first strand: chain 'E' and resid 97 through 99 removed outlier: 7.027A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.079A pdb=" N VAL F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU F 10 " --> pdb=" O GLU F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'F' and resid 47 through 52 removed outlier: 6.120A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY G 10 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AH2, first strand: chain 'G' and resid 97 through 99 removed outlier: 7.026A pdb=" N ARG G 98 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.078A pdb=" N VAL H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU H 10 " --> pdb=" O GLU H 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'H' and resid 47 through 52 removed outlier: 6.119A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AH7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AH9, first strand: chain 'I' and resid 97 through 99 removed outlier: 7.027A pdb=" N ARG I 98 " --> pdb=" O ASP I 108 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2079 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: 14.57 Time building geometry restraints manager: 13.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8545 1.33 - 1.45: 7801 1.45 - 1.58: 14134 1.58 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 30645 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.334 1.231 0.103 2.34e-02 1.83e+03 1.95e+01 bond pdb=" C GLN A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.334 1.231 0.103 2.34e-02 1.83e+03 1.92e+01 bond pdb=" N PRO A 230 " pdb=" CD PRO A 230 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 230 " pdb=" CD PRO B 230 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 ... (remaining 30640 not shown) Histogram of bond angle deviations from ideal: 96.57 - 105.22: 683 105.22 - 113.87: 17966 113.87 - 122.52: 18719 122.52 - 131.17: 4235 131.17 - 139.83: 74 Bond angle restraints: 41677 Sorted by residual: angle pdb=" CA ARG B 102 " pdb=" CB ARG B 102 " pdb=" CG ARG B 102 " ideal model delta sigma weight residual 114.10 101.53 12.57 2.00e+00 2.50e-01 3.95e+01 angle pdb=" CA ARG A 102 " pdb=" CB ARG A 102 " pdb=" CG ARG A 102 " ideal model delta sigma weight residual 114.10 101.55 12.55 2.00e+00 2.50e-01 3.94e+01 angle pdb=" C HIS C 207 " pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 122.36 108.76 13.60 2.42e+00 1.71e-01 3.16e+01 angle pdb=" C CYS C1082 " pdb=" N HIS C1083 " pdb=" CA HIS C1083 " ideal model delta sigma weight residual 121.54 111.00 10.54 1.91e+00 2.74e-01 3.04e+01 angle pdb=" C ILE C 105 " pdb=" N PHE C 106 " pdb=" CA PHE C 106 " ideal model delta sigma weight residual 123.27 113.28 9.99 1.85e+00 2.92e-01 2.92e+01 ... (remaining 41672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 17850 16.43 - 32.86: 849 32.86 - 49.29: 165 49.29 - 65.72: 75 65.72 - 82.15: 17 Dihedral angle restraints: 18956 sinusoidal: 8081 harmonic: 10875 Sorted by residual: dihedral pdb=" CA TRP C 152 " pdb=" C TRP C 152 " pdb=" N MET C 153 " pdb=" CA MET C 153 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA GLU B 96 " pdb=" C GLU B 96 " pdb=" N LYS B 97 " pdb=" CA LYS B 97 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA GLU A 96 " pdb=" C GLU A 96 " pdb=" N LYS A 97 " pdb=" CA LYS A 97 " ideal model delta harmonic sigma weight residual 180.00 134.19 45.81 0 5.00e+00 4.00e-02 8.40e+01 ... (remaining 18953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4834 0.183 - 0.367: 25 0.367 - 0.550: 3 0.550 - 0.734: 0 0.734 - 0.917: 2 Chirality restraints: 4864 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.14e+00 ... (remaining 4861 not shown) Planarity restraints: 5365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " -0.040 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP A 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.040 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP B 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " -0.030 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP C 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.000 2.00e-02 2.50e+03 ... (remaining 5362 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 565 2.53 - 3.13: 27788 3.13 - 3.72: 46285 3.72 - 4.31: 68053 4.31 - 4.90: 108811 Nonbonded interactions: 251502 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 1.944 2.520 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 1.965 2.520 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.011 2.440 nonbonded pdb=" NH2 ARG A 34 " pdb=" O PRO A 217 " model vdw 2.032 2.520 nonbonded pdb=" NH2 ARG B 34 " pdb=" O PRO B 217 " model vdw 2.033 2.520 ... (remaining 251497 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 25 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 1147 or resid 1301 through 1309 \ )) selection = (chain 'B' and (resid 25 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 1147 or resid 1301 through 1309 \ )) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.200 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: 0.030 Extract box with map and model: 20.100 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 90.400 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 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 : 0.014 0.137 30645 Z= 0.919 Angle : 1.222 16.526 41677 Z= 0.650 Chirality : 0.065 0.917 4864 Planarity : 0.007 0.070 5321 Dihedral : 10.999 82.154 11870 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.18 % Favored : 88.25 % Rotamer: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -4.93 (0.10), residues: 3702 helix: -4.75 (0.09), residues: 628 sheet: -3.16 (0.14), residues: 801 loop : -2.97 (0.10), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP A 64 HIS 0.028 0.005 HIS C 207 PHE 0.044 0.005 PHE C 86 TYR 0.046 0.004 TYR C 917 ARG 0.012 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 419 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5414 (m-10) cc_final: 0.4939 (m-80) REVERT: A 380 TYR cc_start: 0.6875 (m-10) cc_final: 0.6636 (m-10) REVERT: A 387 LEU cc_start: 0.7508 (mt) cc_final: 0.7197 (mt) REVERT: A 860 VAL cc_start: 0.7045 (t) cc_final: 0.6729 (p) REVERT: B 30 ASN cc_start: 0.5406 (t0) cc_final: 0.5164 (t0) REVERT: B 902 MET cc_start: 0.8320 (mmm) cc_final: 0.8112 (mmm) REVERT: B 1029 MET cc_start: 0.7885 (tpp) cc_final: 0.7582 (tpp) REVERT: C 106 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: C 396 TYR cc_start: 0.6901 (m-80) cc_final: 0.6532 (m-80) REVERT: I 11 LEU cc_start: 0.3760 (mp) cc_final: 0.3315 (tt) outliers start: 6 outliers final: 1 residues processed: 423 average time/residue: 0.4977 time to fit residues: 315.8996 Evaluate side-chains 203 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain C residue 106 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.7980 chunk 281 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 112 optimal weight: 0.0970 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 337 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 99 ASN A 164 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN A 658 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1119 ASN B 66 HIS B 99 ASN B 164 ASN B 196 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 655 HIS B 658 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS C 134 GLN C 196 ASN C 207 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 57 GLN E 31 ASN F 57 GLN H 56 ASN H 57 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30645 Z= 0.251 Angle : 0.801 13.162 41677 Z= 0.418 Chirality : 0.051 0.705 4864 Planarity : 0.005 0.047 5321 Dihedral : 9.753 59.667 5284 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.08 % Favored : 93.68 % Rotamer: Outliers : 1.30 % Allowed : 5.55 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.12), residues: 3702 helix: -2.03 (0.17), residues: 611 sheet: -2.49 (0.15), residues: 869 loop : -2.47 (0.11), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.008 0.001 HIS A1048 PHE 0.030 0.002 PHE H 35 TYR 0.030 0.002 TYR E 59 ARG 0.005 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 265 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6292 (t80) REVERT: A 860 VAL cc_start: 0.6752 (t) cc_final: 0.6389 (p) REVERT: B 368 LEU cc_start: 0.7016 (mt) cc_final: 0.6758 (mp) REVERT: C 396 TYR cc_start: 0.6214 (m-80) cc_final: 0.5924 (m-10) REVERT: C 489 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.3556 (m-80) REVERT: C 556 ASN cc_start: 0.7282 (p0) cc_final: 0.6909 (p0) REVERT: D 36 MET cc_start: 0.1194 (tpp) cc_final: 0.0492 (tpt) REVERT: F 36 MET cc_start: 0.2935 (mmp) cc_final: 0.2440 (mmp) REVERT: I 11 LEU cc_start: 0.3782 (mp) cc_final: 0.3318 (tt) outliers start: 42 outliers final: 22 residues processed: 295 average time/residue: 0.4724 time to fit residues: 215.4252 Evaluate side-chains 210 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 281 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 338 optimal weight: 30.0000 chunk 365 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 chunk 335 optimal weight: 40.0000 chunk 115 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 99 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 137 ASN C 207 HIS C 245 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 92 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30645 Z= 0.247 Angle : 0.713 12.078 41677 Z= 0.369 Chirality : 0.048 0.601 4864 Planarity : 0.004 0.062 5321 Dihedral : 8.508 55.599 5280 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 1.89 % Allowed : 8.27 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.13), residues: 3702 helix: -0.47 (0.21), residues: 619 sheet: -2.13 (0.15), residues: 861 loop : -2.28 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 64 HIS 0.014 0.001 HIS C 519 PHE 0.032 0.002 PHE H 35 TYR 0.030 0.002 TYR C 144 ARG 0.007 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 221 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 207 HIS cc_start: 0.5699 (m-70) cc_final: 0.5294 (t-90) REVERT: B 374 PHE cc_start: 0.3921 (p90) cc_final: 0.3580 (p90) REVERT: B 869 MET cc_start: 0.6778 (mmm) cc_final: 0.6362 (mmm) REVERT: B 1050 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7493 (ptm) REVERT: C 144 TYR cc_start: 0.3154 (OUTLIER) cc_final: 0.1786 (t80) REVERT: C 489 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.3866 (m-80) REVERT: F 36 MET cc_start: 0.2951 (mmp) cc_final: 0.2424 (mmp) REVERT: H 62 PRO cc_start: 0.5298 (Cg_exo) cc_final: 0.5046 (Cg_endo) REVERT: I 11 LEU cc_start: 0.3479 (mp) cc_final: 0.3077 (tt) outliers start: 61 outliers final: 34 residues processed: 264 average time/residue: 0.4556 time to fit residues: 189.3609 Evaluate side-chains 222 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 chunk 339 optimal weight: 30.0000 chunk 359 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 409 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1119 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 164 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30645 Z= 0.307 Angle : 0.726 12.755 41677 Z= 0.371 Chirality : 0.049 0.578 4864 Planarity : 0.005 0.046 5321 Dihedral : 8.068 59.805 5280 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.75 % Favored : 92.00 % Rotamer: Outliers : 2.63 % Allowed : 8.71 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.13), residues: 3702 helix: 0.02 (0.21), residues: 605 sheet: -1.88 (0.16), residues: 890 loop : -2.22 (0.12), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 64 HIS 0.006 0.002 HIS C 245 PHE 0.026 0.002 PHE A 133 TYR 0.029 0.002 TYR G 57 ARG 0.011 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7112 (t80) REVERT: A 207 HIS cc_start: 0.5991 (m-70) cc_final: 0.5738 (t70) REVERT: B 368 LEU cc_start: 0.6953 (mt) cc_final: 0.6712 (mp) REVERT: C 144 TYR cc_start: 0.2738 (OUTLIER) cc_final: 0.1291 (t80) REVERT: C 489 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.3978 (m-80) REVERT: C 592 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5993 (t80) REVERT: C 1089 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: E 34 MET cc_start: 0.3497 (mmm) cc_final: 0.3284 (mmp) REVERT: H 62 PRO cc_start: 0.5531 (Cg_exo) cc_final: 0.5300 (Cg_endo) REVERT: I 11 LEU cc_start: 0.3407 (mp) cc_final: 0.3073 (tt) outliers start: 85 outliers final: 49 residues processed: 277 average time/residue: 0.4259 time to fit residues: 188.9299 Evaluate side-chains 227 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 101 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 306 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 183 optimal weight: 0.0170 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 125 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30645 Z= 0.195 Angle : 0.644 11.749 41677 Z= 0.330 Chirality : 0.047 0.546 4864 Planarity : 0.004 0.064 5321 Dihedral : 7.275 54.884 5280 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.54 % Favored : 93.19 % Rotamer: Outliers : 2.51 % Allowed : 10.10 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3702 helix: 0.48 (0.22), residues: 607 sheet: -1.59 (0.17), residues: 868 loop : -2.00 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 47 HIS 0.005 0.001 HIS A1048 PHE 0.037 0.002 PHE C 157 TYR 0.024 0.001 TYR G 57 ARG 0.010 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 202 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 904 TYR cc_start: 0.6990 (m-10) cc_final: 0.6767 (m-10) REVERT: B 101 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.5683 (tp) REVERT: B 368 LEU cc_start: 0.7026 (mt) cc_final: 0.6801 (mp) REVERT: C 144 TYR cc_start: 0.2365 (OUTLIER) cc_final: 0.1099 (t80) REVERT: C 462 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7753 (mtmm) REVERT: C 489 TYR cc_start: 0.4645 (OUTLIER) cc_final: 0.4028 (m-80) REVERT: D 20 LEU cc_start: 0.0345 (mt) cc_final: 0.0139 (mp) REVERT: I 11 LEU cc_start: 0.3385 (mp) cc_final: 0.3005 (tt) outliers start: 81 outliers final: 46 residues processed: 261 average time/residue: 0.4520 time to fit residues: 190.7542 Evaluate side-chains 222 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 TRP Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 359 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 166 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 317 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30645 Z= 0.236 Angle : 0.659 12.314 41677 Z= 0.334 Chirality : 0.046 0.548 4864 Planarity : 0.004 0.047 5321 Dihedral : 7.284 61.519 5280 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.43 % Favored : 92.33 % Rotamer: Outliers : 2.17 % Allowed : 10.88 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3702 helix: 0.60 (0.22), residues: 598 sheet: -1.52 (0.17), residues: 892 loop : -1.96 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.037 0.002 PHE C 157 TYR 0.028 0.002 TYR B 351 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 183 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 900 MET cc_start: 0.6962 (mtp) cc_final: 0.6602 (mtp) REVERT: A 904 TYR cc_start: 0.6886 (m-10) cc_final: 0.6622 (m-10) REVERT: B 101 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.5881 (tp) REVERT: C 144 TYR cc_start: 0.2510 (OUTLIER) cc_final: 0.0974 (t80) REVERT: C 462 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7764 (mtmm) REVERT: C 489 TYR cc_start: 0.4547 (OUTLIER) cc_final: 0.3971 (m-80) REVERT: C 592 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5812 (t80) REVERT: I 11 LEU cc_start: 0.3472 (mp) cc_final: 0.3082 (tt) outliers start: 70 outliers final: 56 residues processed: 236 average time/residue: 0.4097 time to fit residues: 158.7550 Evaluate side-chains 224 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 163 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 TRP Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 164 ASN A 409 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30645 Z= 0.285 Angle : 0.669 11.811 41677 Z= 0.341 Chirality : 0.047 0.528 4864 Planarity : 0.004 0.053 5321 Dihedral : 7.486 87.391 5280 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.18 % Favored : 91.57 % Rotamer: Outliers : 2.60 % Allowed : 10.88 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3702 helix: 0.43 (0.21), residues: 619 sheet: -1.53 (0.17), residues: 918 loop : -1.99 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.004 0.001 HIS C 245 PHE 0.036 0.002 PHE C 157 TYR 0.019 0.002 TYR C1067 ARG 0.007 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 183 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 239 GLN cc_start: 0.7731 (tt0) cc_final: 0.7440 (tt0) REVERT: A 900 MET cc_start: 0.7047 (mtp) cc_final: 0.6714 (mtp) REVERT: A 904 TYR cc_start: 0.6908 (m-10) cc_final: 0.6658 (m-10) REVERT: B 101 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6143 (tp) REVERT: B 368 LEU cc_start: 0.6935 (mt) cc_final: 0.6730 (mp) REVERT: B 374 PHE cc_start: 0.5088 (p90) cc_final: 0.4401 (p90) REVERT: C 144 TYR cc_start: 0.2387 (OUTLIER) cc_final: 0.0695 (t80) REVERT: C 462 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7773 (mtmm) REVERT: C 489 TYR cc_start: 0.4578 (OUTLIER) cc_final: 0.4014 (m-80) REVERT: C 1089 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: G 83 MET cc_start: 0.3697 (tpp) cc_final: 0.3382 (tpp) REVERT: I 34 MET cc_start: 0.2520 (mmt) cc_final: 0.2192 (mmt) REVERT: I 74 ASN cc_start: 0.3288 (m-40) cc_final: 0.3058 (m-40) outliers start: 84 outliers final: 62 residues processed: 250 average time/residue: 0.4014 time to fit residues: 166.4037 Evaluate side-chains 235 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 168 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 409 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30645 Z= 0.182 Angle : 0.618 11.062 41677 Z= 0.314 Chirality : 0.045 0.516 4864 Planarity : 0.004 0.068 5321 Dihedral : 7.106 95.893 5280 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.73 % Favored : 92.98 % Rotamer: Outliers : 2.17 % Allowed : 11.31 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3702 helix: 0.73 (0.22), residues: 616 sheet: -1.36 (0.17), residues: 915 loop : -1.87 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.005 0.001 HIS A1048 PHE 0.034 0.001 PHE C 157 TYR 0.022 0.001 TYR B1138 ARG 0.011 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 180 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7381 (t80) REVERT: A 239 GLN cc_start: 0.7710 (tt0) cc_final: 0.7404 (tt0) REVERT: A 900 MET cc_start: 0.6959 (mtp) cc_final: 0.6621 (mtp) REVERT: B 101 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6064 (tp) REVERT: B 374 PHE cc_start: 0.5122 (p90) cc_final: 0.4361 (p90) REVERT: C 144 TYR cc_start: 0.1813 (OUTLIER) cc_final: 0.0260 (t80) REVERT: C 462 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7774 (mtmm) REVERT: C 489 TYR cc_start: 0.4419 (OUTLIER) cc_final: 0.3908 (m-80) REVERT: C 592 PHE cc_start: 0.6174 (t80) cc_final: 0.5967 (t80) REVERT: I 34 MET cc_start: 0.2413 (mmt) cc_final: 0.2124 (mmt) outliers start: 70 outliers final: 49 residues processed: 234 average time/residue: 0.4117 time to fit residues: 158.8506 Evaluate side-chains 211 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 158 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 313 optimal weight: 50.0000 chunk 334 optimal weight: 4.9990 chunk 201 optimal weight: 0.0020 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30645 Z= 0.335 Angle : 0.709 12.081 41677 Z= 0.361 Chirality : 0.048 0.507 4864 Planarity : 0.005 0.059 5321 Dihedral : 7.667 100.417 5280 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.13 % Favored : 90.57 % Rotamer: Outliers : 2.20 % Allowed : 11.65 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3702 helix: 0.24 (0.21), residues: 630 sheet: -1.50 (0.17), residues: 897 loop : -2.00 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 64 HIS 0.005 0.001 HIS B1101 PHE 0.033 0.002 PHE C 157 TYR 0.028 0.002 TYR G 57 ARG 0.011 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 185 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 VAL cc_start: 0.7168 (t) cc_final: 0.6936 (p) REVERT: A 200 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7541 (t80) REVERT: A 239 GLN cc_start: 0.7867 (tt0) cc_final: 0.7638 (tt0) REVERT: B 101 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6563 (tp) REVERT: B 374 PHE cc_start: 0.5341 (p90) cc_final: 0.4574 (p90) REVERT: C 144 TYR cc_start: 0.2150 (OUTLIER) cc_final: 0.0323 (t80) REVERT: C 462 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7790 (mtmm) REVERT: C 489 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.3917 (m-80) REVERT: H 105 THR cc_start: -0.0973 (m) cc_final: -0.1263 (m) REVERT: I 74 ASN cc_start: 0.3247 (m-40) cc_final: 0.2983 (m-40) outliers start: 71 outliers final: 55 residues processed: 238 average time/residue: 0.4222 time to fit residues: 162.4081 Evaluate side-chains 226 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 167 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 101 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 1.9990 chunk 353 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 245 optimal weight: 0.0060 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 40.0000 chunk 295 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 658 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30645 Z= 0.177 Angle : 0.632 11.195 41677 Z= 0.322 Chirality : 0.046 0.509 4864 Planarity : 0.004 0.075 5321 Dihedral : 7.150 103.445 5280 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.37 % Favored : 93.30 % Rotamer: Outliers : 1.67 % Allowed : 12.46 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3702 helix: 0.70 (0.22), residues: 616 sheet: -1.42 (0.17), residues: 912 loop : -1.84 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 47 HIS 0.005 0.001 HIS A1048 PHE 0.037 0.001 PHE A 157 TYR 0.021 0.001 TYR C 144 ARG 0.014 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6297 (tp) REVERT: B 374 PHE cc_start: 0.5095 (p90) cc_final: 0.4556 (p90) REVERT: C 355 ARG cc_start: 0.5568 (ttt90) cc_final: 0.5338 (ttt180) REVERT: C 462 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7793 (mtmm) REVERT: C 489 TYR cc_start: 0.4313 (OUTLIER) cc_final: 0.3866 (m-80) REVERT: I 74 ASN cc_start: 0.3326 (m-40) cc_final: 0.3059 (m-40) outliers start: 54 outliers final: 48 residues processed: 219 average time/residue: 0.4113 time to fit residues: 146.9102 Evaluate side-chains 212 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.6980 chunk 314 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 690 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.092398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068807 restraints weight = 115556.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.070318 restraints weight = 63306.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070852 restraints weight = 40444.562| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30645 Z= 0.215 Angle : 0.635 13.527 41677 Z= 0.322 Chirality : 0.046 0.501 4864 Planarity : 0.004 0.067 5321 Dihedral : 7.077 103.098 5280 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.95 % Rotamer: Outliers : 1.83 % Allowed : 12.52 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.87 (0.14), residues: 3702 helix: 0.72 (0.21), residues: 633 sheet: -1.41 (0.17), residues: 928 loop : -1.82 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.026 0.002 PHE B 133 TYR 0.021 0.001 TYR I 59 ARG 0.013 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5274.26 seconds wall clock time: 100 minutes 27.00 seconds (6027.00 seconds total)