Starting phenix.real_space_refine on Fri Dec 15 08:40:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwm_30483/12_2023/7cwm_30483.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 19532 2.51 5 N 5120 2.21 5 O 5987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 160": "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 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30772 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8253 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 48, 'TRANS': 1007} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8351 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 50, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8350 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 1020} Chain breaks: 6 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.88, per 1000 atoms: 0.55 Number of scatterers: 30772 At special positions: 0 Unit cell: (204.88, 147.68, 170.56, 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 133 16.00 O 5987 8.00 N 5120 7.00 C 19532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 5.9 seconds 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 65 sheets defined 20.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.893A pdb=" N LEU A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.697A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A 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 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.506A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.776A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.023A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.538A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.547A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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: 3.612A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.141A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.323A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.981A 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: 3.723A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.634A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.706A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.881A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.539A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.646A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 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 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.840A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.847A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.450A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.843A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.509A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.275A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.350A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR G 113 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.871A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN J 27 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS K 23 " --> pdb=" O THR K 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR K 74 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA K 25 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR K 72 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N GLN K 27 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP K 70 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2757 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: 14.91 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7469 1.33 - 1.45: 7902 1.45 - 1.58: 15906 1.58 - 1.70: 0 1.70 - 1.83: 169 Bond restraints: 31446 Sorted by residual: bond pdb=" CA SER C 60 " pdb=" CB SER C 60 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.51e-02 4.39e+03 1.46e+01 bond pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.80e-03 1.04e+04 1.44e+01 bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.36e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N GLU C 324 " pdb=" CA GLU C 324 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.16e-02 7.43e+03 1.10e+01 ... (remaining 31441 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.44: 662 105.44 - 112.69: 16568 112.69 - 119.94: 10888 119.94 - 127.18: 14358 127.18 - 134.43: 278 Bond angle restraints: 42754 Sorted by residual: angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS B 301 " pdb=" CA CYS B 301 " pdb=" C CYS B 301 " ideal model delta sigma weight residual 113.23 102.38 10.85 1.24e+00 6.50e-01 7.65e+01 angle pdb=" CA GLY A 283 " pdb=" C GLY A 283 " pdb=" O GLY A 283 " ideal model delta sigma weight residual 122.56 116.30 6.26 1.03e+00 9.43e-01 3.70e+01 angle pdb=" N LEU A 849 " pdb=" CA LEU A 849 " pdb=" C LEU A 849 " ideal model delta sigma weight residual 113.16 106.11 7.05 1.24e+00 6.50e-01 3.23e+01 ... (remaining 42749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 18291 16.86 - 33.71: 739 33.71 - 50.57: 180 50.57 - 67.43: 47 67.43 - 84.28: 9 Dihedral angle restraints: 19266 sinusoidal: 7996 harmonic: 11270 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.01 73.01 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.90 72.90 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.30 72.30 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 19263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 4951 0.315 - 0.630: 10 0.630 - 0.945: 0 0.945 - 1.260: 0 1.260 - 1.575: 1 Chirality restraints: 4962 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.20e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.78e+01 ... (remaining 4959 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.87e+02 pdb=" C7 NAG N 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.262 2.00e-02 2.50e+03 2.24e-01 6.25e+02 pdb=" C7 NAG W 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN C 234 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.192 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.121 2.00e-02 2.50e+03 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 32 2.19 - 2.87: 11790 2.87 - 3.54: 42943 3.54 - 4.22: 72440 4.22 - 4.90: 122122 Nonbonded interactions: 249327 Sorted by model distance: nonbonded pdb=" CG ARG B 408 " pdb=" OG SER L 65 " model vdw 1.512 3.440 nonbonded pdb=" NH2 ARG B 408 " pdb=" CA GLY L 64 " model vdw 1.595 3.520 nonbonded pdb=" CD ARG B 408 " pdb=" OG SER L 65 " model vdw 1.614 3.440 nonbonded pdb=" NH2 ARG B 408 " pdb=" C GLY L 64 " model vdw 1.696 3.350 nonbonded pdb=" NE ARG B 408 " pdb=" OG SER L 65 " model vdw 1.769 2.520 ... (remaining 249322 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 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 518 or (resid 519 \ through 520 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 1 or resid 531 through 698 or (resid 699 and (name N or name CA or name C or nam \ e O or name CB )) or resid 700 through 1147 or resid 1301 through 1305)) selection = (chain 'B' and (resid 14 through 356 or (resid 357 and (name N or name CA or nam \ e C or name O or name CB )) or resid 358 through 378 or resid 389 through 518 or \ (resid 519 through 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 or resid 523 or resid 532 through 698 or (resid 699 and (name N or \ name CA or name C or name O or name CB )) or resid 700 through 1147 or resid 13 \ 01 through 1305)) selection = (chain 'C' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 329 or resid 334 through 378 or re \ sid 389 through 521 or resid 523 or resid 532 through 1147 or resid 1301 through \ 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 0 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = (chain 'K' and (resid 0 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 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: 17.970 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 86.720 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.008 0.069 31446 Z= 0.542 Angle : 1.057 10.848 42754 Z= 0.651 Chirality : 0.068 1.575 4962 Planarity : 0.008 0.281 5464 Dihedral : 10.263 84.284 11901 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 0.54 % Allowed : 1.86 % Favored : 97.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.11), residues: 3827 helix: -3.19 (0.15), residues: 587 sheet: -2.01 (0.16), residues: 816 loop : -2.37 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 47 HIS 0.011 0.002 HIS C1048 PHE 0.035 0.003 PHE C 392 TYR 0.030 0.003 TYR G 94 ARG 0.014 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 272 average time/residue: 0.4965 time to fit residues: 206.3579 Evaluate side-chains 111 residues out of total 3367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2721 time to fit residues: 9.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 20.0000 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 349 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: