Starting phenix.real_space_refine (version: dev) on Mon Feb 27 12:33:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbw_24990/02_2023/7sbw_24990_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30061 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 505 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "J" Number of atoms: 9260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9260 Classifications: {'peptide': 1191} Link IDs: {'PTRANS': 53, 'TRANS': 1137} Chain breaks: 4 Chain: "A" Number of atoms: 9213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9213 Classifications: {'peptide': 1185} Link IDs: {'PTRANS': 53, 'TRANS': 1131} Chain breaks: 5 Chain: "B" Number of atoms: 9287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9287 Classifications: {'peptide': 1196} Link IDs: {'PTRANS': 53, 'TRANS': 1142} Chain breaks: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 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 chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {'8Z9': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'8Z9': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 16.33, per 1000 atoms: 0.54 Number of scatterers: 30061 At special positions: 0 Unit cell: (151.41, 150.38, 193.64, 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 189 16.00 O 5966 8.00 N 4864 7.00 C 19042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.02 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.04 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.10 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.03 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.06 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.04 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.04 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.09 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.04 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.02 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.05 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.02 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.10 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.08 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.06 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.11 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.02 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.12 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.05 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.07 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.04 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.02 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.08 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 787 " " NAG A1403 " - " ASN A 648 " " NAG A1404 " - " ASN A 63 " " NAG B1401 " - " ASN B 713 " " NAG B1402 " - " ASN B 787 " " NAG B1403 " - " ASN B 648 " " NAG B1404 " - " ASN B 63 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 449 " " NAG F 1 " - " ASN J 713 " " NAG G 1 " - " ASN J 738 " " NAG I 1 " - " ASN J 936 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 787 " " NAG J1403 " - " ASN J 648 " " NAG J1404 " - " ASN J 63 " " NAG K 1 " - " ASN J1193 " " NAG M 1 " - " ASN J 206 " " NAG N 1 " - " ASN J 675 " " NAG O 1 " - " ASN J 695 " " NAG P 1 " - " ASN A 137 " " NAG Q 1 " - " ASN A 371 " " NAG R 1 " - " ASN A 713 " " NAG S 1 " - " ASN A 738 " " NAG T 1 " - " ASN A 936 " " NAG U 1 " - " ASN A1193 " " NAG V 1 " - " ASN A 206 " " NAG W 1 " - " ASN A 675 " " NAG X 1 " - " ASN A 695 " " NAG Y 1 " - " ASN A 449 " " NAG Z 1 " - " ASN A1223 " " NAG a 1 " - " ASN B 137 " " NAG b 1 " - " ASN B 212 " " NAG c 1 " - " ASN B 371 " " NAG d 1 " - " ASN B 449 " " NAG e 1 " - " ASN B 738 " " NAG f 1 " - " ASN B 936 " " NAG g 1 " - " ASN B1193 " " NAG h 1 " - " ASN B 206 " " NAG i 1 " - " ASN B 675 " " NAG j 1 " - " ASN B 695 " Time building additional restraints: 12.94 Conformation dependent library (CDL) restraints added in 4.5 seconds 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 56 sheets defined 23.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'J' and resid 92 through 95 Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 302 through 310 Processing helix chain 'J' and resid 345 through 349 Processing helix chain 'J' and resid 357 through 359 No H-bonds generated for 'chain 'J' and resid 357 through 359' Processing helix chain 'J' and resid 372 through 378 Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 414 through 417 Processing helix chain 'J' and resid 425 through 428 No H-bonds generated for 'chain 'J' and resid 425 through 428' Processing helix chain 'J' and resid 447 through 449 No H-bonds generated for 'chain 'J' and resid 447 through 449' Processing helix chain 'J' and resid 459 through 463 Processing helix chain 'J' and resid 468 through 471 No H-bonds generated for 'chain 'J' and resid 468 through 471' Processing helix chain 'J' and resid 531 through 533 No H-bonds generated for 'chain 'J' and resid 531 through 533' Processing helix chain 'J' and resid 568 through 570 No H-bonds generated for 'chain 'J' and resid 568 through 570' Processing helix chain 'J' and resid 580 through 582 No H-bonds generated for 'chain 'J' and resid 580 through 582' Processing helix chain 'J' and resid 708 through 713 Processing helix chain 'J' and resid 825 through 829 Processing helix chain 'J' and resid 834 through 873 removed outlier: 3.654A pdb=" N VAL J 841 " --> pdb=" O LYS J 837 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR J 843 " --> pdb=" O GLN J 839 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N SER J 845 " --> pdb=" O VAL J 841 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE J 846 " --> pdb=" O GLU J 842 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 880 through 883 Processing helix chain 'J' and resid 914 through 921 Processing helix chain 'J' and resid 927 through 936 removed outlier: 3.696A pdb=" N ASN J 936 " --> pdb=" O ALA J 932 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 953 Processing helix chain 'J' and resid 964 through 978 removed outlier: 4.130A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 984 through 986 No H-bonds generated for 'chain 'J' and resid 984 through 986' Processing helix chain 'J' and resid 991 through 1002 removed outlier: 3.779A pdb=" N LEU J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) Processing helix chain 'J' and resid 1006 through 1011 Processing helix chain 'J' and resid 1013 through 1030 Processing helix chain 'J' and resid 1036 through 1060 removed outlier: 4.052A pdb=" N LEU J1059 " --> pdb=" O LEU J1055 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER J1060 " --> pdb=" O LEU J1056 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1076 Processing helix chain 'J' and resid 1079 through 1124 removed outlier: 4.863A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) Processing helix chain 'J' and resid 1211 through 1213 No H-bonds generated for 'chain 'J' and resid 1211 through 1213' Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 873 removed outlier: 4.594A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 883 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.762A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 953 Processing helix chain 'A' and resid 964 through 978 removed outlier: 4.099A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.727A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1030 Processing helix chain 'A' and resid 1036 through 1060 removed outlier: 3.756A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 4.839A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.394A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'B' and resid 425 through 428 No H-bonds generated for 'chain 'B' and resid 425 through 428' Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.828A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 825 through 829 Processing helix chain 'B' and resid 834 through 873 removed outlier: 3.619A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 884 Processing helix chain 'B' and resid 914 through 921 Processing helix chain 'B' and resid 927 through 936 removed outlier: 3.738A pdb=" N ASN B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 953 Processing helix chain 'B' and resid 964 through 979 removed outlier: 4.033A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 986 No H-bonds generated for 'chain 'B' and resid 984 through 986' Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.711A pdb=" N LEU B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1030 removed outlier: 3.704A pdb=" N GLN B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1060 removed outlier: 4.041A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1124 removed outlier: 4.807A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing sheet with id= A, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= B, first strand: chain 'H' and resid 114 through 116 removed outlier: 5.380A pdb=" N UNK H 37 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N UNK H 45 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N UNK H 39 " --> pdb=" O UNK H 43 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N UNK H 43 " --> pdb=" O UNK H 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= D, first strand: chain 'L' and resid 18 through 21 Processing sheet with id= E, first strand: chain 'J' and resid 42 through 44 Processing sheet with id= F, first strand: chain 'J' and resid 64 through 72 removed outlier: 3.603A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 100 through 102 removed outlier: 3.831A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 272 through 276 removed outlier: 5.484A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 116 through 118 Processing sheet with id= J, first strand: chain 'J' and resid 318 through 321 removed outlier: 3.502A pdb=" N CYS J 732 " --> pdb=" O PHE J 703 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 332 through 335 removed outlier: 8.023A pdb=" N VAL J 333 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN J 632 " --> pdb=" O VAL J 333 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG J 335 " --> pdb=" O ASN J 632 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP J 634 " --> pdb=" O ARG J 335 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 353 through 355 removed outlier: 6.133A pdb=" N SER J 451 " --> pdb=" O VAL J 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.609A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 484 through 488 Processing sheet with id= O, first strand: chain 'J' and resid 491 through 493 removed outlier: 4.272A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 773 through 777 removed outlier: 6.429A pdb=" N VAL J 757 " --> pdb=" O THR J 750 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR J 750 " --> pdb=" O VAL J 757 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 805 through 815 Processing sheet with id= R, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.099A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 1225 through 1227 Processing sheet with id= T, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id= U, first strand: chain 'H' and resid 92 through 94 removed outlier: 3.546A pdb=" N UNK H 109 " --> pdb=" O UNK H 93 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 797 through 804 removed outlier: 6.551A pdb=" N LYS J1164 " --> pdb=" O SER J 803 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= X, first strand: chain 'A' and resid 64 through 73 removed outlier: 3.563A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.511A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= AA, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.581A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= AC, first strand: chain 'A' and resid 332 through 335 removed outlier: 8.110A pdb=" N VAL A 333 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 632 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ARG A 335 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP A 634 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.176A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.400A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= AG, first strand: chain 'A' and resid 773 through 777 removed outlier: 6.214A pdb=" N VAL A 757 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR A 750 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 805 through 815 Processing sheet with id= AI, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.192A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 1225 through 1227 Processing sheet with id= AK, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AL, first strand: chain 'A' and resid 797 through 804 removed outlier: 6.559A pdb=" N LYS A1164 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AN, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= AO, first strand: chain 'B' and resid 64 through 73 removed outlier: 3.859A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.778A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= AR, first strand: chain 'B' and resid 252 through 255 removed outlier: 3.976A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 177 through 179 No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= AU, first strand: chain 'B' and resid 332 through 335 removed outlier: 8.268A pdb=" N VAL B 333 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 632 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ARG B 335 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 634 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.079A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.613A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AY, first strand: chain 'B' and resid 755 through 759 Processing sheet with id= AZ, first strand: chain 'B' and resid 805 through 815 Processing sheet with id= BA, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.200A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= BC, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id= BD, first strand: chain 'B' and resid 797 through 804 removed outlier: 6.503A pdb=" N LYS B1164 " --> pdb=" O SER B 803 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2877 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: 14.46 Time building geometry restraints manager: 13.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5860 1.31 - 1.45: 10528 1.45 - 1.59: 14065 1.59 - 1.73: 14 1.73 - 1.87: 234 Bond restraints: 30701 Sorted by residual: bond pdb=" CB HIS J 219 " pdb=" CG HIS J 219 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CB HIS B 219 " pdb=" CG HIS B 219 " ideal model delta sigma weight residual 1.497 1.411 0.086 1.40e-02 5.10e+03 3.81e+01 bond pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sigma weight residual 1.523 1.583 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" CB HIS B 490 " pdb=" CG HIS B 490 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.23e+01 bond pdb=" C3 NAG R 2 " pdb=" C4 NAG R 2 " ideal model delta sigma weight residual 1.523 1.578 -0.055 1.00e-02 1.00e+04 3.08e+01 ... (remaining 30696 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.42: 388 103.42 - 111.08: 11692 111.08 - 118.74: 12773 118.74 - 126.40: 16726 126.40 - 134.07: 239 Bond angle restraints: 41818 Sorted by residual: angle pdb=" N PRO B 981 " pdb=" CA PRO B 981 " pdb=" C PRO B 981 " ideal model delta sigma weight residual 110.70 122.53 -11.83 1.22e+00 6.72e-01 9.41e+01 angle pdb=" N PRO J 981 " pdb=" CA PRO J 981 " pdb=" C PRO J 981 " ideal model delta sigma weight residual 110.70 122.40 -11.70 1.22e+00 6.72e-01 9.19e+01 angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.18 -11.48 1.22e+00 6.72e-01 8.85e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 129.00 -8.97 9.90e-01 1.02e+00 8.21e+01 angle pdb=" N VAL A 608 " pdb=" CA VAL A 608 " pdb=" C VAL A 608 " ideal model delta sigma weight residual 110.72 119.52 -8.80 1.01e+00 9.80e-01 7.60e+01 ... (remaining 41813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 17955 33.53 - 67.07: 196 67.07 - 100.60: 32 100.60 - 134.14: 3 134.14 - 167.67: 1 Dihedral angle restraints: 18187 sinusoidal: 7105 harmonic: 11082 Sorted by residual: dihedral pdb=" CB CYS A1125 " pdb=" SG CYS A1125 " pdb=" SG CYS A1136 " pdb=" CB CYS A1136 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B1125 " pdb=" SG CYS B1125 " pdb=" SG CYS B1136 " pdb=" CB CYS B1136 " ideal model delta sinusoidal sigma weight residual 93.00 173.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 45.80 47.20 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 18184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3796 0.110 - 0.220: 1033 0.220 - 0.330: 148 0.330 - 0.440: 15 0.440 - 0.550: 5 Chirality restraints: 4997 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.97e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.79e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.78e+02 ... (remaining 4994 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 738 " -0.067 2.00e-02 2.50e+03 6.94e-02 6.02e+01 pdb=" CG ASN B 738 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 738 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 738 " 0.106 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 449 " -0.043 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN A 449 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 449 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 449 " 0.074 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 192 " 0.062 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP A 192 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 192 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 192 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 192 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A 192 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 192 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 192 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 192 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 192 " 0.031 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9786 2.82 - 3.34: 27397 3.34 - 3.86: 50568 3.86 - 4.38: 61343 4.38 - 4.90: 99325 Nonbonded interactions: 248419 Sorted by model distance: nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.302 2.520 nonbonded pdb=" O CYS J 937 " pdb=" OH TYR J 952 " model vdw 2.302 2.440 nonbonded pdb=" N ASN J 371 " pdb=" OD1 ASN J 371 " model vdw 2.326 2.520 nonbonded pdb=" OH TYR J 737 " pdb=" OG1 THR J 770 " model vdw 2.341 2.440 nonbonded pdb=" OG SER J 662 " pdb=" OG1 THR B 64 " model vdw 2.363 2.440 ... (remaining 248414 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 15 through 1233 or resid 1401 through 1404)) selection = (chain 'B' and (resid 15 through 32 or resid 36 through 150 or resid 157 through \ 505 or resid 517 through 902 or resid 909 through 1233 or resid 1401 through 14 \ 04)) selection = (chain 'J' and (resid 15 through 32 or resid 36 through 505 or resid 517 through \ 762 or resid 771 through 1233 or resid 1401 through 1404)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'c' selection = chain 'h' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = (chain 'H' and resid 18 through 118) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 19042 2.51 5 N 4864 2.21 5 O 5966 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.090 Check model and map are aligned: 0.440 Process input model: 79.390 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.300 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 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 : 0.022 0.142 30701 Z= 1.452 Angle : 1.699 11.835 41818 Z= 1.155 Chirality : 0.100 0.550 4997 Planarity : 0.009 0.038 5301 Dihedral : 10.598 167.670 10896 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.06 % 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: 0.46 (0.13), residues: 3542 helix: -0.16 (0.16), residues: 820 sheet: 0.78 (0.16), residues: 848 loop : 0.46 (0.14), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 375 time to evaluate : 3.624 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 outliers start: 13 outliers final: 9 residues processed: 388 average time/residue: 0.4802 time to fit residues: 289.0784 Evaluate side-chains 156 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 3.423 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 9 average time/residue: 0.2661 time to fit residues: 8.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 157 ASN J 219 HIS J 418 GLN J 483 HIS J 663 ASN J 762 ASN J 849 ASN J1042 GLN J1057 GLN A 252 HIS A 411 ASN A 483 HIS A 532 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 724 ASN A 745 GLN A 839 GLN A 849 ASN A1103 GLN B 32 ASN B 171 ASN B 219 HIS B 252 HIS B 483 HIS B 532 HIS B 839 GLN B1057 GLN B1071 GLN B1103 GLN B1138 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 30701 Z= 0.295 Angle : 0.634 10.515 41818 Z= 0.349 Chirality : 0.047 0.630 4997 Planarity : 0.004 0.049 5301 Dihedral : 7.344 157.558 4670 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 1.06 % 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: 0.73 (0.14), residues: 3542 helix: 1.47 (0.19), residues: 803 sheet: 0.68 (0.17), residues: 796 loop : 0.07 (0.14), residues: 1943 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 4.010 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 outliers start: 33 outliers final: 16 residues processed: 218 average time/residue: 0.3988 time to fit residues: 146.4151 Evaluate side-chains 157 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 3.167 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.2605 time to fit residues: 12.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 233 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 370 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 340 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 HIS J 663 ASN J1057 GLN A 186 ASN A 411 ASN A 532 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A 839 GLN B 32 ASN B 532 HIS B 839 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 30701 Z= 0.251 Angle : 0.553 11.594 41818 Z= 0.304 Chirality : 0.045 0.698 4997 Planarity : 0.004 0.044 5301 Dihedral : 6.419 145.585 4670 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.84 % 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: 0.68 (0.14), residues: 3542 helix: 1.86 (0.19), residues: 786 sheet: 0.58 (0.17), residues: 797 loop : -0.14 (0.14), residues: 1959 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 182 average time/residue: 0.4048 time to fit residues: 124.8433 Evaluate side-chains 145 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 3.324 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 12 average time/residue: 0.2893 time to fit residues: 10.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 344 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 HIS A 532 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 849 ASN B 32 ASN B 475 GLN B 777 ASN B1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 30701 Z= 0.401 Angle : 0.599 12.288 41818 Z= 0.326 Chirality : 0.047 0.671 4997 Planarity : 0.005 0.054 5301 Dihedral : 6.318 133.585 4670 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.90 % 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: 0.39 (0.14), residues: 3542 helix: 1.66 (0.19), residues: 789 sheet: 0.46 (0.17), residues: 762 loop : -0.37 (0.13), residues: 1991 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 0.4090 time to fit residues: 115.0279 Evaluate side-chains 145 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 3.437 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 15 average time/residue: 0.2880 time to fit residues: 12.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 HIS J 719 GLN J 777 ASN A 532 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 30701 Z= 0.427 Angle : 0.599 11.459 41818 Z= 0.325 Chirality : 0.047 0.686 4997 Planarity : 0.005 0.057 5301 Dihedral : 6.161 100.743 4670 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3542 helix: 1.55 (0.19), residues: 789 sheet: 0.30 (0.17), residues: 758 loop : -0.54 (0.13), residues: 1995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.4267 time to fit residues: 120.5020 Evaluate side-chains 143 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 3.429 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.2765 time to fit residues: 13.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 0.8980 chunk 302 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 719 GLN A 724 ASN A 996 GLN A1057 GLN B 950 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30701 Z= 0.166 Angle : 0.492 12.019 41818 Z= 0.267 Chirality : 0.043 0.638 4997 Planarity : 0.004 0.052 5301 Dihedral : 5.426 57.579 4670 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.39 % 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: 0.40 (0.14), residues: 3542 helix: 1.86 (0.19), residues: 788 sheet: 0.47 (0.17), residues: 783 loop : -0.46 (0.14), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.4162 time to fit residues: 111.3880 Evaluate side-chains 140 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 3.638 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.3919 time to fit residues: 9.4956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 266 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 307 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 719 GLN A 724 ASN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 30701 Z= 0.349 Angle : 0.549 10.890 41818 Z= 0.297 Chirality : 0.045 0.652 4997 Planarity : 0.004 0.056 5301 Dihedral : 5.579 55.707 4670 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3542 helix: 1.73 (0.19), residues: 795 sheet: 0.32 (0.17), residues: 776 loop : -0.50 (0.14), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 154 average time/residue: 0.4392 time to fit residues: 116.4775 Evaluate side-chains 134 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 3.409 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 0.3128 time to fit residues: 12.7216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 231 optimal weight: 0.0050 chunk 247 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 719 GLN A 724 ASN A 839 GLN A1057 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 30701 Z= 0.140 Angle : 0.474 11.093 41818 Z= 0.257 Chirality : 0.042 0.641 4997 Planarity : 0.004 0.052 5301 Dihedral : 5.155 46.394 4670 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.39 % 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: 0.44 (0.14), residues: 3542 helix: 2.01 (0.20), residues: 788 sheet: 0.43 (0.18), residues: 786 loop : -0.46 (0.14), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 150 average time/residue: 0.4405 time to fit residues: 112.1501 Evaluate side-chains 130 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 3.376 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.2961 time to fit residues: 7.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 0.7980 chunk 317 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 337 optimal weight: 0.7980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 461 ASN J 719 GLN A 724 ASN A1057 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 30701 Z= 0.455 Angle : 0.593 10.693 41818 Z= 0.318 Chirality : 0.046 0.655 4997 Planarity : 0.005 0.060 5301 Dihedral : 5.650 51.109 4670 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.52 % 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: 0.19 (0.14), residues: 3542 helix: 1.72 (0.19), residues: 783 sheet: 0.31 (0.18), residues: 762 loop : -0.59 (0.14), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.4352 time to fit residues: 101.2807 Evaluate side-chains 129 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 3.742 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 0.3227 time to fit residues: 11.0659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 375 optimal weight: 0.8980 chunk 345 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 719 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A1057 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN B1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 30701 Z= 0.151 Angle : 0.486 10.677 41818 Z= 0.264 Chirality : 0.043 0.629 4997 Planarity : 0.004 0.053 5301 Dihedral : 5.246 46.554 4670 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.26 % 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: 0.35 (0.14), residues: 3542 helix: 1.96 (0.19), residues: 788 sheet: 0.37 (0.18), residues: 776 loop : -0.52 (0.14), residues: 1978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7084 Ramachandran restraints generated. 3542 Oldfield, 0 Emsley, 3542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.4322 time to fit residues: 101.5424 Evaluate side-chains 127 residues out of total 3105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 3.529 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.2847 time to fit residues: 7.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 307 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 719 GLN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.061113 restraints weight = 65605.444| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.75 r_work: 0.2585 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 30701 Z= 0.342 Angle : 0.541 10.622 41818 Z= 0.292 Chirality : 0.045 0.641 4997 Planarity : 0.004 0.056 5301 Dihedral : 5.446 47.752 4670 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.19 % 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: 0.28 (0.14), residues: 3542 helix: 1.86 (0.19), residues: 784 sheet: 0.34 (0.18), residues: 780 loop : -0.55 (0.14), residues: 1978 =============================================================================== Job complete usr+sys time: 5046.34 seconds wall clock time: 94 minutes 29.63 seconds (5669.63 seconds total)