Starting phenix.real_space_refine on Thu Mar 21 09:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v23_31635/03_2024/7v23_31635_neut.pdb" } resolution = 2.96 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= 0.070 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 134 5.16 5 C 18814 2.51 5 N 4881 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "O ARG 87": "NH1" <-> "NH2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ASP 113": "OD1" <-> "OD2" Residue "R GLU 3": "OE1" <-> "OE2" Residue "R TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S ARG 87": "NH1" <-> "NH2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "T GLU 3": "OE1" <-> "OE2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29633 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7879 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 55, 'TRANS': 962} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 8011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8011 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 7917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7917 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 55, 'TRANS': 975} Chain breaks: 7 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "T" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 14.56, per 1000 atoms: 0.49 Number of scatterers: 29633 At special positions: 0 Unit cell: (195.48, 193.32, 192.24, 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 134 16.00 O 5804 8.00 N 4881 7.00 C 18814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 87 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM29085 O5 NAG H 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29141 O5 NAG K 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29113 O5 NAG J 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29323 O5 NAG A1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM29225 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " 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-ASN " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " 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 B 717 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 5.5 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 67 sheets defined 22.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.664A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.519A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.355A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.700A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.793A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.668A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.947A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.576A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.827A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.594A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.640A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.874A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.619A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.761A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.941A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.634A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.624A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.417A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.749A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.602A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.143A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.587A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.729A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.506A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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: 3.747A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.640A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.861A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 30 removed outlier: 3.566A pdb=" N SER O 30 " --> pdb=" O PHE O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 65 Processing helix chain 'O' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP O 107 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER O 108 " --> pdb=" O SER O 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR O 110 " --> pdb=" O TRP O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 30 removed outlier: 3.589A pdb=" N ASP P 29 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU P 82 " --> pdb=" O ALA P 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.567A pdb=" N SER Q 30 " --> pdb=" O PHE Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP Q 107 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER Q 108 " --> pdb=" O SER Q 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR Q 110 " --> pdb=" O TRP Q 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.590A pdb=" N ASP R 29 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU R 82 " --> pdb=" O ALA R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 30 removed outlier: 3.567A pdb=" N SER S 30 " --> pdb=" O PHE S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 103 through 110 removed outlier: 3.790A pdb=" N TRP S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER S 108 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR S 110 " --> pdb=" O TRP S 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 30 removed outlier: 3.589A pdb=" N ASP T 29 " --> pdb=" O LYS T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 82 removed outlier: 3.885A pdb=" N GLU T 82 " --> pdb=" O ALA T 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.601A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.353A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 removed outlier: 10.237A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 160 removed outlier: 10.237A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.455A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.258A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.970A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.437A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.972A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.119A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.686A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.907A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 154 through 157 removed outlier: 4.765A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 157 removed outlier: 4.765A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.797A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.631A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.547A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.334A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.826A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.489A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.514A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.563A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.504A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.138A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.240A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.661A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.053A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.568A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG O 38 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU O 46 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL O 114 " --> pdb=" O THR O 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 18 through 20 removed outlier: 4.358A pdb=" N THR P 69 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER P 66 " --> pdb=" O THR P 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'Q' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET Q 34 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL Q 114 " --> pdb=" O THR Q 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 18 through 20 removed outlier: 4.359A pdb=" N THR R 69 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER R 66 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 44 through 47 removed outlier: 6.480A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 44 through 47 removed outlier: 6.480A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'S' and resid 11 through 12 removed outlier: 7.256A pdb=" N MET S 34 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG S 38 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU S 46 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.725A pdb=" N VAL S 114 " --> pdb=" O THR S 98 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 18 through 20 removed outlier: 4.359A pdb=" N THR T 69 " --> pdb=" O SER T 66 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER T 66 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'T' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 44 through 47 removed outlier: 6.479A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3210 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: 14.39 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 11594 1.38 - 1.61: 18527 1.61 - 1.84: 175 1.84 - 2.07: 5 2.07 - 2.30: 1 Bond restraints: 30302 Sorted by residual: bond pdb=" CB ASN A1074 " pdb=" CG ASN A1074 " ideal model delta sigma weight residual 1.516 2.305 -0.789 2.50e-02 1.60e+03 9.96e+02 bond pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 1.328 1.904 -0.576 2.10e-02 2.27e+03 7.53e+02 bond pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta sigma weight residual 1.527 1.804 -0.277 1.30e-02 5.92e+03 4.55e+02 bond pdb=" C GLU A1072 " pdb=" N LYS A1073 " ideal model delta sigma weight residual 1.332 1.522 -0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" N ASN A1074 " pdb=" CA ASN A1074 " ideal model delta sigma weight residual 1.459 1.621 -0.162 1.27e-02 6.20e+03 1.63e+02 ... (remaining 30297 not shown) Histogram of bond angle deviations from ideal: 94.51 - 106.66: 1049 106.66 - 118.80: 23338 118.80 - 130.95: 16799 130.95 - 143.09: 91 143.09 - 155.24: 3 Bond angle restraints: 41280 Sorted by residual: angle pdb=" C LYS T 52 " pdb=" N ARG T 53 " pdb=" CA ARG T 53 " ideal model delta sigma weight residual 122.06 155.24 -33.18 1.78e+00 3.16e-01 3.47e+02 angle pdb=" C LYS R 52 " pdb=" N ARG R 53 " pdb=" CA ARG R 53 " ideal model delta sigma weight residual 122.06 155.20 -33.14 1.78e+00 3.16e-01 3.47e+02 angle pdb=" C LYS P 52 " pdb=" N ARG P 53 " pdb=" CA ARG P 53 " ideal model delta sigma weight residual 122.06 155.12 -33.06 1.78e+00 3.16e-01 3.45e+02 angle pdb=" N GLU A1072 " pdb=" CA GLU A1072 " pdb=" C GLU A1072 " ideal model delta sigma weight residual 109.23 127.53 -18.30 1.55e+00 4.16e-01 1.39e+02 angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta sigma weight residual 110.37 128.75 -18.38 1.65e+00 3.67e-01 1.24e+02 ... (remaining 41275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16765 17.97 - 35.94: 1300 35.94 - 53.90: 423 53.90 - 71.87: 78 71.87 - 89.84: 47 Dihedral angle restraints: 18613 sinusoidal: 7677 harmonic: 10936 Sorted by residual: dihedral pdb=" N ASN A1074 " pdb=" C ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta harmonic sigma weight residual 122.80 157.98 -35.18 0 2.50e+00 1.60e-01 1.98e+02 dihedral pdb=" C ASN A1074 " pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta harmonic sigma weight residual -122.60 -152.22 29.62 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" CA ASN A1074 " pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta harmonic sigma weight residual 180.00 122.51 57.49 0 5.00e+00 4.00e-02 1.32e+02 ... (remaining 18610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 4825 0.977 - 1.955: 2 1.955 - 2.932: 0 2.932 - 3.909: 0 3.909 - 4.887: 1 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 2.49 -4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CA ASN A1074 " pdb=" N ASN A1074 " pdb=" C ASN A1074 " pdb=" CB ASN A1074 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.05e+01 ... (remaining 4825 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.058 2.00e-02 2.50e+03 5.81e-02 4.21e+01 pdb=" CG ASN A 331 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.061 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.001 2.00e-02 2.50e+03 5.77e-02 4.17e+01 pdb=" CG ASN A 709 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 331 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ASN A 331 " 0.092 2.00e-02 2.50e+03 pdb=" O ASN A 331 " -0.035 2.00e-02 2.50e+03 pdb=" N ILE A 332 " -0.031 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 46 2.27 - 2.93: 13560 2.93 - 3.59: 41717 3.59 - 4.24: 67324 4.24 - 4.90: 114631 Nonbonded interactions: 237278 Sorted by model distance: nonbonded pdb=" ND2 ASN A1074 " pdb=" C5 NAG H 1 " model vdw 1.613 2.840 nonbonded pdb=" OE1 GLN C1071 " pdb=" O7 NAG L 1 " model vdw 1.944 3.040 nonbonded pdb=" OD2 ASP A 578 " pdb=" N THR A 581 " model vdw 1.986 2.520 nonbonded pdb=" CG ASN A1074 " pdb=" C5 NAG H 1 " model vdw 2.004 3.700 nonbonded pdb=" O SER Q 52 " pdb=" NH1 ARG Q 72 " model vdw 2.016 2.520 ... (remaining 237273 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 14 through 331 or (resid 332 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 344 or (resid 345 t \ hrough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 363 or (resid 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 373 or (res \ id 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thr \ ough 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 449 and (name N or name CA or name C or n \ ame O or name CB )) or resid 450 through 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 504 or (res \ id 505 and (name N or name CA or name C or name O or name CB )) or resid 506 thr \ ough 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 620 or resid 641 through 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 14 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or na \ me CA or name C or name O or name CB )) or resid 399 through 426 or (resid 427 t \ hrough 428 and (name N or name CA or name C or name O or name CB )) or resid 429 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or resi \ d 503 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 throu \ gh 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 454 or resid 491 th \ rough 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) \ or resid 506 through 1146 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.250 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 80.730 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.789 30302 Z= 0.709 Angle : 1.152 33.180 41280 Z= 0.630 Chirality : 0.097 4.887 4828 Planarity : 0.007 0.091 5272 Dihedral : 15.052 89.841 11454 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.00 % Favored : 92.79 % Rotamer: Outliers : 3.68 % Allowed : 0.91 % Favored : 95.41 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3716 helix: 0.07 (0.19), residues: 736 sheet: -0.62 (0.17), residues: 903 loop : -1.52 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP S 115 HIS 0.018 0.002 HIS B 66 PHE 0.061 0.003 PHE A1075 TYR 0.041 0.002 TYR A 904 ARG 0.059 0.002 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 440 time to evaluate : 3.247 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: B 150 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6406 (mmmm) REVERT: B 388 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.5400 (t0) REVERT: B 747 THR cc_start: 0.8074 (m) cc_final: 0.7552 (m) REVERT: B 751 ASN cc_start: 0.7571 (m-40) cc_final: 0.7341 (m-40) REVERT: O 4 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3623 (mt) REVERT: O 57 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6184 (mp10) REVERT: O 112 MET cc_start: 0.7256 (mtp) cc_final: 0.6452 (ptt) REVERT: P 52 LYS cc_start: 0.8233 (mttt) cc_final: 0.7993 (mttp) REVERT: P 104 THR cc_start: 0.3513 (OUTLIER) cc_final: 0.3177 (p) REVERT: Q 73 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6363 (t70) REVERT: Q 80 TYR cc_start: 0.6749 (m-10) cc_final: 0.6500 (m-80) REVERT: Q 87 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5308 (mtm180) REVERT: R 62 SER cc_start: 0.7069 (OUTLIER) cc_final: 0.6648 (m) REVERT: R 73 THR cc_start: 0.6356 (m) cc_final: 0.6156 (p) REVERT: R 74 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.3608 (tp) REVERT: R 80 MET cc_start: 0.6013 (mtp) cc_final: 0.5487 (tmt) outliers start: 117 outliers final: 12 residues processed: 500 average time/residue: 1.0437 time to fit residues: 643.0286 Evaluate side-chains 300 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 280 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 57 GLN Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 87 ARG Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain T residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 926 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 856 ASN B1005 GLN B1083 HIS B1088 HIS B1106 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1083 HIS C1135 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** Q 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 30302 Z= 0.309 Angle : 0.824 30.048 41280 Z= 0.402 Chirality : 0.071 2.426 4828 Planarity : 0.006 0.083 5272 Dihedral : 10.108 122.289 5073 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 2.76 % Allowed : 10.59 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.92 (0.13), residues: 3716 helix: 0.68 (0.20), residues: 705 sheet: -0.22 (0.17), residues: 922 loop : -1.26 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP O 115 HIS 0.005 0.001 HIS C 66 PHE 0.056 0.002 PHE A1075 TYR 0.021 0.002 TYR S 94 ARG 0.011 0.001 ARG T 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 356 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6383 (m-10) cc_final: 0.6127 (m-10) REVERT: A 740 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.5957 (ptm) REVERT: A 747 THR cc_start: 0.8198 (m) cc_final: 0.7619 (p) REVERT: B 747 THR cc_start: 0.8173 (m) cc_final: 0.7599 (m) REVERT: B 751 ASN cc_start: 0.7813 (m-40) cc_final: 0.7483 (m-40) REVERT: B 1109 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 246 ARG cc_start: 0.6408 (mmt90) cc_final: 0.5928 (mmm-85) REVERT: C 754 LEU cc_start: 0.8926 (mt) cc_final: 0.8663 (mt) REVERT: O 95 TYR cc_start: 0.4930 (m-10) cc_final: 0.4437 (m-10) REVERT: P 48 TYR cc_start: 0.7132 (p90) cc_final: 0.6908 (p90) REVERT: P 52 LYS cc_start: 0.8228 (mttt) cc_final: 0.7716 (mmtp) REVERT: Q 27 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.6065 (m-10) REVERT: Q 36 TRP cc_start: 0.5130 (m100) cc_final: 0.4522 (m100) REVERT: Q 72 ARG cc_start: 0.3547 (ptm160) cc_final: 0.3285 (ptm160) REVERT: Q 87 ARG cc_start: 0.6687 (mmt-90) cc_final: 0.5652 (mmp-170) REVERT: Q 93 VAL cc_start: 0.7105 (p) cc_final: 0.6795 (t) REVERT: Q 98 THR cc_start: 0.5751 (p) cc_final: 0.4897 (p) REVERT: R 80 MET cc_start: 0.5937 (mtp) cc_final: 0.5413 (tmt) REVERT: S 29 PHE cc_start: 0.5000 (t80) cc_final: 0.4725 (t80) REVERT: S 80 TYR cc_start: 0.4887 (m-80) cc_final: 0.4642 (m-80) REVERT: T 34 TRP cc_start: 0.5242 (m100) cc_final: 0.4991 (m100) outliers start: 88 outliers final: 32 residues processed: 415 average time/residue: 0.9873 time to fit residues: 511.9489 Evaluate side-chains 291 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 256 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 281 optimal weight: 0.3980 chunk 230 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 302 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 218 GLN B 856 ASN B1083 HIS B1088 HIS B1101 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 710 ASN C 955 ASN C1036 GLN C1083 HIS ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN Q 35 ASN Q 99 ASN ** Q 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 30302 Z= 0.218 Angle : 0.695 24.300 41280 Z= 0.346 Chirality : 0.058 1.777 4828 Planarity : 0.005 0.084 5272 Dihedral : 8.928 96.449 5039 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.67 % Allowed : 13.85 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.69 (0.14), residues: 3716 helix: 1.01 (0.20), residues: 702 sheet: -0.25 (0.16), residues: 982 loop : -1.09 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 107 HIS 0.007 0.001 HIS A1083 PHE 0.042 0.002 PHE O 29 TYR 0.027 0.001 TYR R 48 ARG 0.007 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 317 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7563 (pp20) REVERT: A 394 ASN cc_start: 0.4749 (m-40) cc_final: 0.4371 (m110) REVERT: A 740 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6334 (ptm) REVERT: A 1050 MET cc_start: 0.8329 (ptm) cc_final: 0.8104 (ptp) REVERT: B 152 TRP cc_start: 0.2780 (OUTLIER) cc_final: 0.2511 (m100) REVERT: B 747 THR cc_start: 0.8254 (m) cc_final: 0.7861 (m) REVERT: B 751 ASN cc_start: 0.7893 (m-40) cc_final: 0.7601 (m-40) REVERT: B 1109 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: C 246 ARG cc_start: 0.6720 (mmt90) cc_final: 0.5956 (mmm-85) REVERT: C 754 LEU cc_start: 0.8964 (mt) cc_final: 0.8731 (mt) REVERT: O 29 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.6122 (t80) REVERT: O 95 TYR cc_start: 0.4804 (m-10) cc_final: 0.4439 (m-10) REVERT: O 112 MET cc_start: 0.5930 (mtt) cc_final: 0.5535 (mtp) REVERT: O 115 TRP cc_start: 0.4983 (OUTLIER) cc_final: 0.3620 (t-100) REVERT: P 52 LYS cc_start: 0.8194 (mttt) cc_final: 0.7813 (mtmm) REVERT: Q 32 TYR cc_start: 0.5497 (m-80) cc_final: 0.5087 (m-80) REVERT: Q 36 TRP cc_start: 0.5051 (m100) cc_final: 0.4372 (m100) REVERT: Q 72 ARG cc_start: 0.3477 (ptm160) cc_final: 0.3237 (ptm160) REVERT: Q 80 TYR cc_start: 0.5859 (m-80) cc_final: 0.5618 (m-80) REVERT: Q 87 ARG cc_start: 0.6637 (mmt-90) cc_final: 0.5884 (mmm160) REVERT: Q 93 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6704 (t) REVERT: R 80 MET cc_start: 0.5894 (mtp) cc_final: 0.5362 (tmt) REVERT: S 80 TYR cc_start: 0.4927 (m-80) cc_final: 0.4671 (m-80) REVERT: S 98 THR cc_start: 0.5216 (p) cc_final: 0.4913 (p) REVERT: T 34 TRP cc_start: 0.5224 (m100) cc_final: 0.5008 (m100) outliers start: 85 outliers final: 35 residues processed: 381 average time/residue: 0.9701 time to fit residues: 468.7476 Evaluate side-chains 310 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 268 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 360 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 322 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A1002 GLN B 207 HIS B 211 ASN B 856 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1088 HIS B1101 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 675 GLN C1083 HIS C1142 GLN ** O 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN Q 103 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30302 Z= 0.259 Angle : 0.681 32.124 41280 Z= 0.338 Chirality : 0.052 1.412 4828 Planarity : 0.005 0.100 5272 Dihedral : 8.083 95.772 5039 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.78 % Rotamer: Outliers : 3.58 % Allowed : 15.58 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3716 helix: 1.15 (0.21), residues: 694 sheet: -0.23 (0.16), residues: 974 loop : -1.08 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 107 HIS 0.008 0.001 HIS A1083 PHE 0.032 0.002 PHE B 565 TYR 0.020 0.001 TYR P 35 ARG 0.010 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 308 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7471 (tp30) cc_final: 0.7113 (tm-30) REVERT: A 224 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: B 78 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6723 (ttp-110) REVERT: B 132 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7027 (pp20) REVERT: B 152 TRP cc_start: 0.2849 (OUTLIER) cc_final: 0.2550 (m100) REVERT: B 564 GLN cc_start: 0.6825 (pt0) cc_final: 0.6524 (pt0) REVERT: B 987 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7786 (Cg_endo) REVERT: B 988 GLU cc_start: 0.7524 (pp20) cc_final: 0.7248 (pm20) REVERT: C 646 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6848 (tpt90) REVERT: O 95 TYR cc_start: 0.4583 (m-10) cc_final: 0.3944 (m-10) REVERT: O 115 TRP cc_start: 0.4758 (OUTLIER) cc_final: 0.3067 (t-100) REVERT: P 52 LYS cc_start: 0.8230 (mttt) cc_final: 0.7668 (mmtm) REVERT: Q 29 PHE cc_start: 0.6164 (t80) cc_final: 0.5843 (t80) REVERT: Q 32 TYR cc_start: 0.6339 (m-80) cc_final: 0.5844 (m-80) REVERT: Q 87 ARG cc_start: 0.6384 (mmt-90) cc_final: 0.5568 (mmm160) REVERT: Q 93 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6802 (t) REVERT: S 80 TYR cc_start: 0.4806 (m-80) cc_final: 0.4577 (m-80) REVERT: T 20 ILE cc_start: 0.1331 (OUTLIER) cc_final: 0.1124 (mt) REVERT: T 34 TRP cc_start: 0.5314 (m100) cc_final: 0.5052 (m100) outliers start: 114 outliers final: 52 residues processed: 396 average time/residue: 0.8998 time to fit residues: 451.2124 Evaluate side-chains 311 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 254 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 856 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 675 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 30302 Z= 0.447 Angle : 0.767 23.550 41280 Z= 0.388 Chirality : 0.053 1.135 4828 Planarity : 0.006 0.109 5272 Dihedral : 8.068 93.505 5038 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer: Outliers : 4.62 % Allowed : 16.43 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.00 (0.13), residues: 3716 helix: 0.62 (0.20), residues: 721 sheet: -0.43 (0.16), residues: 994 loop : -1.26 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP O 107 HIS 0.012 0.002 HIS B1088 PHE 0.046 0.003 PHE B 565 TYR 0.025 0.002 TYR A1067 ARG 0.008 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 305 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7790 (tp30) cc_final: 0.7323 (tm-30) REVERT: A 224 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: A 1050 MET cc_start: 0.8430 (ptm) cc_final: 0.8196 (ptp) REVERT: A 1139 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6151 (t0) REVERT: B 132 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7198 (pp20) REVERT: B 152 TRP cc_start: 0.2859 (OUTLIER) cc_final: 0.2476 (m100) REVERT: B 677 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: B 900 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7655 (mtm) REVERT: C 389 ASP cc_start: 0.8262 (t0) cc_final: 0.8014 (m-30) REVERT: C 429 PHE cc_start: 0.8369 (t80) cc_final: 0.8136 (t80) REVERT: C 646 ARG cc_start: 0.7514 (tpm170) cc_final: 0.7275 (tpt90) REVERT: O 95 TYR cc_start: 0.4586 (m-10) cc_final: 0.3400 (m-80) REVERT: O 115 TRP cc_start: 0.5100 (OUTLIER) cc_final: 0.2732 (t-100) REVERT: P 26 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7077 (ptmt) REVERT: P 35 TYR cc_start: 0.5417 (m-10) cc_final: 0.5214 (m-10) REVERT: P 52 LYS cc_start: 0.8288 (mttt) cc_final: 0.7941 (mtmm) REVERT: Q 29 PHE cc_start: 0.6285 (t80) cc_final: 0.5597 (t80) REVERT: Q 32 TYR cc_start: 0.6177 (m-80) cc_final: 0.5760 (m-80) REVERT: Q 87 ARG cc_start: 0.6345 (mmt-90) cc_final: 0.5480 (mmm160) REVERT: Q 93 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6872 (t) REVERT: R 16 GLN cc_start: 0.2855 (OUTLIER) cc_final: 0.2401 (mt0) REVERT: S 72 ARG cc_start: 0.4238 (OUTLIER) cc_final: 0.3834 (mmm-85) REVERT: S 80 TYR cc_start: 0.5091 (m-80) cc_final: 0.4816 (m-80) REVERT: T 20 ILE cc_start: 0.1365 (OUTLIER) cc_final: 0.1129 (mt) REVERT: T 45 LEU cc_start: 0.2767 (OUTLIER) cc_final: 0.2400 (mm) outliers start: 147 outliers final: 69 residues processed: 419 average time/residue: 0.9772 time to fit residues: 513.6431 Evaluate side-chains 331 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 250 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 26 LYS Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 21 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.8980 chunk 324 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 360 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1083 HIS B 146 HIS B 211 ASN B 239 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1083 HIS ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30302 Z= 0.198 Angle : 0.650 15.628 41280 Z= 0.325 Chirality : 0.048 0.930 4828 Planarity : 0.005 0.077 5272 Dihedral : 7.496 90.060 5038 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.36 % Allowed : 19.51 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3716 helix: 0.94 (0.20), residues: 715 sheet: -0.28 (0.16), residues: 959 loop : -1.21 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 107 HIS 0.004 0.001 HIS B1088 PHE 0.023 0.001 PHE B 565 TYR 0.022 0.001 TYR C1138 ARG 0.010 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 288 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8149 (m-80) cc_final: 0.7937 (m-80) REVERT: A 224 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7442 (pp20) REVERT: A 1074 ASN cc_start: 0.2642 (OUTLIER) cc_final: 0.2237 (t0) REVERT: B 17 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5247 (m-40) REVERT: B 132 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7399 (pp20) REVERT: B 152 TRP cc_start: 0.2984 (OUTLIER) cc_final: 0.2729 (m100) REVERT: B 582 LEU cc_start: 0.8651 (tt) cc_final: 0.8051 (mm) REVERT: C 133 PHE cc_start: 0.7162 (m-80) cc_final: 0.6658 (m-80) REVERT: C 246 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6001 (mmt90) REVERT: C 429 PHE cc_start: 0.8380 (t80) cc_final: 0.8036 (t80) REVERT: C 646 ARG cc_start: 0.7535 (tpm170) cc_final: 0.7152 (tpt90) REVERT: C 752 LEU cc_start: 0.8812 (pp) cc_final: 0.8533 (pp) REVERT: O 95 TYR cc_start: 0.4459 (m-80) cc_final: 0.3368 (m-80) REVERT: O 115 TRP cc_start: 0.4978 (OUTLIER) cc_final: 0.2608 (t-100) REVERT: P 34 TRP cc_start: 0.5198 (m100) cc_final: 0.4684 (m100) REVERT: P 52 LYS cc_start: 0.8198 (mttt) cc_final: 0.7849 (mttp) REVERT: Q 29 PHE cc_start: 0.6179 (t80) cc_final: 0.5608 (t80) REVERT: Q 32 TYR cc_start: 0.6140 (m-80) cc_final: 0.5645 (m-80) REVERT: Q 87 ARG cc_start: 0.6561 (mmt-90) cc_final: 0.5589 (mmm160) REVERT: Q 93 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6939 (t) REVERT: S 80 TYR cc_start: 0.4850 (m-80) cc_final: 0.4594 (m-80) outliers start: 107 outliers final: 43 residues processed: 378 average time/residue: 0.9690 time to fit residues: 458.1362 Evaluate side-chains 298 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 303 optimal weight: 0.4980 chunk 201 optimal weight: 0.3980 chunk 359 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1002 GLN A1005 GLN A1083 HIS A1142 GLN B 211 ASN B 856 ASN B1005 GLN B1101 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 606 ASN C 675 GLN C 677 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30302 Z= 0.281 Angle : 0.669 16.530 41280 Z= 0.335 Chirality : 0.049 0.854 4828 Planarity : 0.005 0.132 5272 Dihedral : 7.279 90.364 5038 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.52 % Allowed : 19.70 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3716 helix: 0.96 (0.20), residues: 721 sheet: -0.31 (0.15), residues: 992 loop : -1.22 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 107 HIS 0.007 0.001 HIS B1088 PHE 0.031 0.002 PHE A 106 TYR 0.034 0.001 TYR A 904 ARG 0.013 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 265 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 224 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: B 132 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7356 (pp20) REVERT: B 152 TRP cc_start: 0.2997 (OUTLIER) cc_final: 0.2717 (m100) REVERT: B 388 ASN cc_start: 0.7426 (m-40) cc_final: 0.6658 (t0) REVERT: B 429 PHE cc_start: 0.7255 (t80) cc_final: 0.7046 (t80) REVERT: B 434 ILE cc_start: 0.5693 (OUTLIER) cc_final: 0.5316 (pt) REVERT: B 1005 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: C 133 PHE cc_start: 0.7268 (m-80) cc_final: 0.6679 (m-80) REVERT: C 246 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6003 (mmt90) REVERT: C 646 ARG cc_start: 0.7586 (tpm170) cc_final: 0.7180 (tpt90) REVERT: O 57 GLN cc_start: 0.7154 (mp10) cc_final: 0.6326 (mp10) REVERT: O 95 TYR cc_start: 0.4767 (m-80) cc_final: 0.3548 (m-80) REVERT: O 104 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7130 (t) REVERT: O 115 TRP cc_start: 0.5114 (OUTLIER) cc_final: 0.2481 (t-100) REVERT: P 34 TRP cc_start: 0.5041 (m100) cc_final: 0.4750 (m100) REVERT: P 52 LYS cc_start: 0.8186 (mttt) cc_final: 0.7844 (mttp) REVERT: Q 29 PHE cc_start: 0.6180 (t80) cc_final: 0.5654 (t80) REVERT: Q 32 TYR cc_start: 0.6169 (m-80) cc_final: 0.5707 (m-80) REVERT: Q 87 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.5468 (mmm160) REVERT: Q 93 VAL cc_start: 0.7245 (OUTLIER) cc_final: 0.6950 (t) REVERT: S 80 TYR cc_start: 0.4879 (m-80) cc_final: 0.4618 (m-80) outliers start: 112 outliers final: 58 residues processed: 356 average time/residue: 1.0326 time to fit residues: 455.1086 Evaluate side-chains 314 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1005 GLN A1083 HIS A1101 HIS B 211 ASN B 920 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 580 GLN C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1135 ASN O 74 ASN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN S 57 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30302 Z= 0.293 Angle : 0.671 14.157 41280 Z= 0.336 Chirality : 0.049 0.820 4828 Planarity : 0.005 0.099 5272 Dihedral : 7.089 90.297 5038 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.11 % Allowed : 20.39 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 3716 helix: 0.89 (0.20), residues: 722 sheet: -0.32 (0.15), residues: 975 loop : -1.22 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 34 HIS 0.036 0.002 HIS C 245 PHE 0.028 0.002 PHE C 855 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.001 ARG Q 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 266 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7381 (pp20) REVERT: B 132 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7306 (pp20) REVERT: B 152 TRP cc_start: 0.2929 (OUTLIER) cc_final: 0.2672 (m100) REVERT: B 388 ASN cc_start: 0.8030 (m-40) cc_final: 0.7244 (t0) REVERT: C 133 PHE cc_start: 0.7327 (m-80) cc_final: 0.6737 (m-80) REVERT: C 988 GLU cc_start: 0.8023 (pp20) cc_final: 0.7693 (pp20) REVERT: O 57 GLN cc_start: 0.7215 (mp10) cc_final: 0.6363 (mp10) REVERT: O 83 MET cc_start: 0.2539 (tpp) cc_final: 0.1476 (mtp) REVERT: O 95 TYR cc_start: 0.4680 (m-80) cc_final: 0.3594 (m-80) REVERT: O 104 SER cc_start: 0.7430 (OUTLIER) cc_final: 0.7158 (t) REVERT: O 115 TRP cc_start: 0.5063 (OUTLIER) cc_final: 0.2456 (t-100) REVERT: P 34 TRP cc_start: 0.4939 (m100) cc_final: 0.4640 (m100) REVERT: P 35 TYR cc_start: 0.6060 (m-80) cc_final: 0.5640 (m-80) REVERT: P 52 LYS cc_start: 0.8249 (mttt) cc_final: 0.7939 (mttp) REVERT: Q 29 PHE cc_start: 0.6175 (t80) cc_final: 0.5610 (t80) REVERT: Q 32 TYR cc_start: 0.6225 (m-80) cc_final: 0.5743 (m-80) REVERT: Q 87 ARG cc_start: 0.6511 (mmt-90) cc_final: 0.5476 (mmm160) REVERT: Q 93 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6923 (t) REVERT: S 80 TYR cc_start: 0.4892 (m-80) cc_final: 0.4630 (m-80) REVERT: T 20 ILE cc_start: 0.1349 (OUTLIER) cc_final: 0.0992 (mt) REVERT: T 41 GLN cc_start: 0.5142 (mt0) cc_final: 0.4634 (mp10) REVERT: T 80 MET cc_start: 0.4172 (OUTLIER) cc_final: 0.3832 (mmm) outliers start: 99 outliers final: 62 residues processed: 350 average time/residue: 0.9961 time to fit residues: 436.7639 Evaluate side-chains 314 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 245 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 ASP Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 302 optimal weight: 0.8980 chunk 316 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 613 GLN A 641 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 211 ASN B 544 ASN B 580 GLN B 690 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.156 30302 Z= 0.499 Angle : 0.781 16.312 41280 Z= 0.394 Chirality : 0.053 0.812 4828 Planarity : 0.006 0.105 5272 Dihedral : 7.450 89.796 5038 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.62 % Favored : 92.36 % Rotamer: Outliers : 3.49 % Allowed : 20.74 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.13 (0.13), residues: 3716 helix: 0.51 (0.19), residues: 732 sheet: -0.50 (0.15), residues: 980 loop : -1.36 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A1102 HIS 0.023 0.002 HIS A1101 PHE 0.035 0.003 PHE C 106 TYR 0.027 0.002 TYR C 170 ARG 0.008 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 269 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1101 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6607 (m-70) REVERT: B 132 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7337 (pp20) REVERT: B 152 TRP cc_start: 0.2969 (OUTLIER) cc_final: 0.2626 (m100) REVERT: B 388 ASN cc_start: 0.8047 (m-40) cc_final: 0.7225 (t0) REVERT: C 133 PHE cc_start: 0.7432 (m-80) cc_final: 0.6960 (m-80) REVERT: C 242 LEU cc_start: 0.8040 (mt) cc_final: 0.7778 (mt) REVERT: C 1130 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8108 (mt) REVERT: O 57 GLN cc_start: 0.7222 (mp10) cc_final: 0.6411 (mp10) REVERT: O 83 MET cc_start: 0.2752 (tpp) cc_final: 0.2117 (tpp) REVERT: O 95 TYR cc_start: 0.4901 (m-80) cc_final: 0.3705 (m-80) REVERT: O 112 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4799 (mtt) REVERT: O 115 TRP cc_start: 0.5219 (OUTLIER) cc_final: 0.2688 (t-100) REVERT: P 34 TRP cc_start: 0.4905 (m100) cc_final: 0.4616 (m100) REVERT: P 52 LYS cc_start: 0.8290 (mttt) cc_final: 0.7956 (mttp) REVERT: Q 29 PHE cc_start: 0.6188 (t80) cc_final: 0.5630 (t80) REVERT: Q 32 TYR cc_start: 0.6351 (m-80) cc_final: 0.5874 (m-80) REVERT: Q 73 ASP cc_start: 0.6662 (m-30) cc_final: 0.6287 (t70) REVERT: Q 87 ARG cc_start: 0.6519 (mmt-90) cc_final: 0.5483 (mmm160) REVERT: Q 93 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6891 (t) REVERT: R 16 GLN cc_start: 0.3155 (OUTLIER) cc_final: 0.2764 (mt0) REVERT: S 80 TYR cc_start: 0.5042 (m-80) cc_final: 0.4671 (m-80) REVERT: T 20 ILE cc_start: 0.1498 (OUTLIER) cc_final: 0.1205 (mt) REVERT: T 41 GLN cc_start: 0.5399 (mt0) cc_final: 0.4724 (mp10) REVERT: T 80 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.4273 (mmm) outliers start: 111 outliers final: 63 residues processed: 357 average time/residue: 1.0004 time to fit residues: 446.1680 Evaluate side-chains 299 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 228 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 901 GLN A1005 GLN A1101 HIS B 211 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 388 ASN C 394 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30302 Z= 0.232 Angle : 0.673 16.896 41280 Z= 0.336 Chirality : 0.048 0.678 4828 Planarity : 0.005 0.063 5272 Dihedral : 7.059 90.362 5038 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.26 % Allowed : 22.02 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3716 helix: 0.77 (0.20), residues: 722 sheet: -0.43 (0.15), residues: 976 loop : -1.25 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 34 HIS 0.012 0.001 HIS A1101 PHE 0.032 0.002 PHE B 106 TYR 0.028 0.001 TYR C 170 ARG 0.009 0.001 ARG A 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 249 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7226 (pp20) REVERT: A 747 THR cc_start: 0.8342 (m) cc_final: 0.8135 (p) REVERT: B 132 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7417 (pp20) REVERT: B 152 TRP cc_start: 0.2905 (OUTLIER) cc_final: 0.2691 (m100) REVERT: B 564 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6310 (mt0) REVERT: C 133 PHE cc_start: 0.7396 (m-80) cc_final: 0.6933 (m-80) REVERT: C 242 LEU cc_start: 0.8085 (mt) cc_final: 0.7804 (mt) REVERT: C 507 PRO cc_start: 0.6584 (Cg_exo) cc_final: 0.6296 (Cg_endo) REVERT: C 1040 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 1130 ILE cc_start: 0.8412 (pt) cc_final: 0.8148 (mt) REVERT: O 95 TYR cc_start: 0.4921 (m-80) cc_final: 0.3836 (m-80) REVERT: O 112 MET cc_start: 0.5040 (OUTLIER) cc_final: 0.4736 (mtt) REVERT: O 115 TRP cc_start: 0.5084 (OUTLIER) cc_final: 0.2738 (t-100) REVERT: P 34 TRP cc_start: 0.4741 (m100) cc_final: 0.4524 (m100) REVERT: P 52 LYS cc_start: 0.8204 (mttt) cc_final: 0.7897 (mttp) REVERT: Q 3 GLN cc_start: 0.6559 (mm110) cc_final: 0.6085 (tm-30) REVERT: Q 29 PHE cc_start: 0.6066 (t80) cc_final: 0.5498 (t80) REVERT: Q 32 TYR cc_start: 0.6245 (m-80) cc_final: 0.5730 (m-80) REVERT: Q 73 ASP cc_start: 0.6655 (m-30) cc_final: 0.6298 (t70) REVERT: Q 87 ARG cc_start: 0.6530 (mmt-90) cc_final: 0.5514 (mmm160) REVERT: Q 93 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6944 (t) REVERT: R 16 GLN cc_start: 0.2757 (OUTLIER) cc_final: 0.2394 (mt0) REVERT: S 80 TYR cc_start: 0.4818 (m-80) cc_final: 0.4451 (m-80) REVERT: T 41 GLN cc_start: 0.5110 (mt0) cc_final: 0.4462 (mp10) REVERT: T 80 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.4391 (mmm) outliers start: 72 outliers final: 47 residues processed: 306 average time/residue: 0.9831 time to fit residues: 376.2035 Evaluate side-chains 295 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 115 TRP Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 115 TRP Chi-restraints excluded: chain R residue 16 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 80 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 304 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1002 GLN A1005 GLN B 211 ASN B 388 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 394 ASN C 422 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.151000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096758 restraints weight = 55767.570| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.81 r_work: 0.3236 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30302 Z= 0.242 Angle : 0.657 15.131 41280 Z= 0.327 Chirality : 0.047 0.620 4828 Planarity : 0.005 0.060 5272 Dihedral : 6.862 88.258 5038 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.20 % Allowed : 22.37 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3716 helix: 0.79 (0.20), residues: 735 sheet: -0.38 (0.15), residues: 985 loop : -1.21 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 34 HIS 0.007 0.001 HIS B1088 PHE 0.041 0.002 PHE C 429 TYR 0.016 0.001 TYR A1067 ARG 0.010 0.001 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10392.89 seconds wall clock time: 186 minutes 4.67 seconds (11164.67 seconds total)