Starting phenix.real_space_refine on Fri Apr 12 14:50:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/04_2024/7soe_25268.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 16305 2.51 5 N 4473 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25947 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7222 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 56, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1157 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 24, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 539 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 530 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 631 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7222 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 56, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1157 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 24, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 539 Chain: "D" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 530 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 631 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "F" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7222 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 56, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1157 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 24, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 539 Chain: "G" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 530 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 631 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 171 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "F" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 14.44, per 1000 atoms: 0.56 Number of scatterers: 25947 At special positions: 0 Unit cell: (202.32, 187.146, 171.972, 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 126 16.00 O 5043 8.00 N 4473 7.00 C 16305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS C 985 " distance=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.14 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.12 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS F 383 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.07 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS F 985 " distance=2.00 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.14 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.12 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.07 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.02 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.11 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.01 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.05 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.14 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.12 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.01 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.07 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 165 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 149 " " NAG A1316 " - " ASN A 17 " " NAG A1317 " - " ASN A 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG C1315 " - " ASN C 149 " " NAG C1316 " - " ASN C 17 " " NAG C1317 " - " ASN C 343 " " NAG F1301 " - " ASN F 331 " " NAG F1302 " - " ASN F 603 " " NAG F1303 " - " ASN F 657 " " NAG F1304 " - " ASN F1074 " " NAG F1305 " - " ASN F1098 " " NAG F1306 " - " ASN F1134 " " NAG F1307 " - " ASN F 616 " " NAG F1308 " - " ASN F 709 " " NAG F1309 " - " ASN F 801 " " NAG F1310 " - " ASN F 717 " " NAG F1311 " - " ASN F 61 " " NAG F1312 " - " ASN F 282 " " NAG F1313 " - " ASN F 165 " " NAG F1314 " - " ASN F 234 " " NAG F1315 " - " ASN F 149 " " NAG F1316 " - " ASN F 17 " " NAG F1317 " - " ASN F 343 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN C 122 " " NAG K 1 " - " ASN F 122 " Time building additional restraints: 10.39 Conformation dependent library (CDL) restraints added in 5.2 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 21.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.595A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.655A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.758A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.104A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.000A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.823A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.595A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.655A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.758A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.104A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.000A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.823A pdb=" N GLU D 82 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.595A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.654A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 620 Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.758A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 853 through 856 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 940 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.754A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.000A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 994 " --> pdb=" O GLU F 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.824A pdb=" N GLU G 82 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.231A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 132 current: chain 'A' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 158 current: chain 'B' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 61 current: chain 'B' and resid 108 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.874A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.538A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.000A pdb=" N ILE A 788 " --> pdb=" O ASN F 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.563A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.231A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 132 current: chain 'C' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 158 current: chain 'E' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 61 current: chain 'E' and resid 108 through 115 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.873A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.537A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.564A pdb=" N TRP D 34 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'F' and resid 27 through 31 removed outlier: 8.230A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N HIS F 207 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N ALA F 222 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.714A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 83 through 85 current: chain 'F' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 126 through 132 current: chain 'F' and resid 151 through 158 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 151 through 158 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 108 through 115 Processing sheet with id=AE5, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.362A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 324 through 328 removed outlier: 4.232A pdb=" N GLU F 324 " --> pdb=" O CYS F 538 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.873A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.537A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.684A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 718 through 728 removed outlier: 5.963A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.563A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 1180 hydrogen bonds defined for protein. 3180 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: 13.35 Time building geometry restraints manager: 11.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4778 1.32 - 1.45: 6499 1.45 - 1.57: 15015 1.57 - 1.70: 3 1.70 - 1.83: 150 Bond restraints: 26445 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.18e+01 bond pdb=" C PRO A 986 " pdb=" O PRO A 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.17e+01 bond pdb=" C PRO F 986 " pdb=" O PRO F 986 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.16e+01 bond pdb=" N CYS A 985 " pdb=" CA CYS A 985 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.25e-02 6.40e+03 9.81e+00 bond pdb=" N CYS F 985 " pdb=" CA CYS F 985 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.25e-02 6.40e+03 9.74e+00 ... (remaining 26440 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.62: 873 105.62 - 112.69: 14070 112.69 - 119.76: 7058 119.76 - 126.83: 14159 126.83 - 133.90: 152 Bond angle restraints: 36312 Sorted by residual: angle pdb=" N PRO F 986 " pdb=" CA PRO F 986 " pdb=" C PRO F 986 " ideal model delta sigma weight residual 110.70 123.55 -12.85 1.22e+00 6.72e-01 1.11e+02 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 123.53 -12.83 1.22e+00 6.72e-01 1.11e+02 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 123.51 -12.81 1.22e+00 6.72e-01 1.10e+02 angle pdb=" C LEU F 861 " pdb=" N PRO F 862 " pdb=" CA PRO F 862 " ideal model delta sigma weight residual 119.66 126.23 -6.57 7.20e-01 1.93e+00 8.33e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.20e-01 1.93e+00 8.25e+01 ... (remaining 36307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 15942 17.50 - 34.99: 393 34.99 - 52.49: 60 52.49 - 69.99: 42 69.99 - 87.48: 18 Dihedral angle restraints: 16455 sinusoidal: 5547 harmonic: 10908 Sorted by residual: dihedral pdb=" C ASN A 540 " pdb=" N ASN A 540 " pdb=" CA ASN A 540 " pdb=" CB ASN A 540 " ideal model delta harmonic sigma weight residual -122.60 -111.84 -10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C ASN F 540 " pdb=" N ASN F 540 " pdb=" CA ASN F 540 " pdb=" CB ASN F 540 " ideal model delta harmonic sigma weight residual -122.60 -111.84 -10.76 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C ASN C 540 " pdb=" N ASN C 540 " pdb=" CA ASN C 540 " pdb=" CB ASN C 540 " ideal model delta harmonic sigma weight residual -122.60 -111.86 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 16452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4080 0.104 - 0.208: 327 0.208 - 0.312: 60 0.312 - 0.416: 15 0.416 - 0.519: 9 Chirality restraints: 4491 Sorted by residual: chirality pdb=" C1 NAG C1317 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1317 " pdb=" O5 NAG C1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" C1 NAG F1317 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG F1317 " pdb=" O5 NAG F1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" C1 NAG A1317 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1317 " pdb=" O5 NAG A1317 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 4488 not shown) Planarity restraints: 4857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.043 2.00e-02 2.50e+03 4.47e-02 2.49e+01 pdb=" CG ASN A1074 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.043 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN C1074 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F1074 " -0.043 2.00e-02 2.50e+03 4.45e-02 2.47e+01 pdb=" CG ASN F1074 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN F1074 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F1074 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " -0.053 2.00e-02 2.50e+03 ... (remaining 4854 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 10940 2.91 - 3.41: 22424 3.41 - 3.91: 40963 3.91 - 4.40: 44555 4.40 - 4.90: 76032 Nonbonded interactions: 194914 Sorted by model distance: nonbonded pdb=" O GLU A 988 " pdb=" OE1 GLU A 988 " model vdw 2.416 3.040 nonbonded pdb=" O GLU C 988 " pdb=" OE1 GLU C 988 " model vdw 2.417 3.040 nonbonded pdb=" O GLU F 988 " pdb=" OE1 GLU F 988 " model vdw 2.417 3.040 nonbonded pdb=" ND2 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.539 2.520 nonbonded pdb=" ND2 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.539 2.520 ... (remaining 194909 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' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.590 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: 29.240 Check model and map are aligned: 0.480 Set scattering table: 0.000 Process input model: 73.160 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.010 0.059 26445 Z= 0.709 Angle : 1.291 12.846 36312 Z= 0.878 Chirality : 0.073 0.519 4491 Planarity : 0.005 0.030 4803 Dihedral : 9.440 87.485 9246 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.15 % Allowed : 0.89 % Favored : 98.96 % 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: 0.29 (0.13), residues: 3717 helix: 0.36 (0.18), residues: 675 sheet: 1.07 (0.16), residues: 981 loop : -0.25 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.005 TRP A1102 HIS 0.006 0.001 HIS C1071 PHE 0.025 0.004 PHE A 329 TYR 0.036 0.004 TYR F1067 ARG 0.003 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 401 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 780 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7253 (tp30) outliers start: 3 outliers final: 0 residues processed: 401 average time/residue: 1.2624 time to fit residues: 596.2819 Evaluate side-chains 265 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 340 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 607 GLN A 641 ASN A 644 GLN A 658 ASN A 779 GLN A 901 GLN A 935 GLN A 955 ASN A1005 GLN A1010 GLN C 540 ASN C 544 ASN C 606 ASN C 607 GLN C 641 ASN C 658 ASN C 779 GLN C 901 GLN C 935 GLN C 955 ASN C1002 GLN C1005 GLN C1010 GLN F 540 ASN F 544 ASN F 641 ASN F 644 GLN F 658 ASN F 779 GLN F 901 GLN F 935 GLN F 955 ASN F1002 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26445 Z= 0.234 Angle : 0.559 7.774 36312 Z= 0.305 Chirality : 0.047 0.229 4491 Planarity : 0.004 0.033 4803 Dihedral : 4.383 26.362 5118 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.93 % Allowed : 6.94 % Favored : 90.13 % 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: 0.92 (0.13), residues: 3717 helix: 1.94 (0.20), residues: 648 sheet: 1.28 (0.16), residues: 984 loop : -0.12 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1102 HIS 0.006 0.001 HIS F 655 PHE 0.016 0.002 PHE F 392 TYR 0.022 0.002 TYR A1067 ARG 0.008 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7865 (tt0) cc_final: 0.7481 (tt0) REVERT: A 785 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7993 (m) REVERT: C 305 SER cc_start: 0.7388 (OUTLIER) cc_final: 0.7095 (p) REVERT: C 785 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7936 (m) REVERT: F 759 PHE cc_start: 0.7782 (m-10) cc_final: 0.7411 (m-10) REVERT: F 785 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8010 (m) outliers start: 59 outliers final: 34 residues processed: 308 average time/residue: 1.1970 time to fit residues: 438.2050 Evaluate side-chains 281 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 368 optimal weight: 40.0000 chunk 303 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 116 optimal weight: 30.0000 chunk 273 optimal weight: 0.0040 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 607 GLN A 613 GLN A 644 GLN A 779 GLN A 935 GLN A1002 GLN A1005 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN C1010 GLN F 314 GLN F 613 GLN F 644 GLN F 856 ASN F1002 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26445 Z= 0.208 Angle : 0.528 6.668 36312 Z= 0.279 Chirality : 0.046 0.223 4491 Planarity : 0.004 0.036 4803 Dihedral : 4.125 24.224 5118 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.72 % Allowed : 7.24 % Favored : 89.04 % 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: 0.94 (0.13), residues: 3717 helix: 2.15 (0.20), residues: 645 sheet: 1.38 (0.16), residues: 984 loop : -0.22 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1102 HIS 0.009 0.001 HIS A 655 PHE 0.017 0.002 PHE F 55 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.001 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 250 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7882 (tt0) cc_final: 0.7381 (tt0) REVERT: C 305 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.7105 (p) REVERT: F 947 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: F 964 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7599 (mtmt) outliers start: 75 outliers final: 37 residues processed: 282 average time/residue: 1.2259 time to fit residues: 409.9641 Evaluate side-chains 275 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 881 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 947 LYS Chi-restraints excluded: chain F residue 964 LYS Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 229 optimal weight: 0.3980 chunk 342 optimal weight: 1.9990 chunk 362 optimal weight: 0.3980 chunk 178 optimal weight: 0.0980 chunk 324 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A1005 GLN C 314 GLN C 607 GLN C 613 GLN C 804 GLN C 935 GLN C1002 GLN C1005 GLN C1010 GLN F 935 GLN F1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26445 Z= 0.178 Angle : 0.500 6.467 36312 Z= 0.261 Chirality : 0.046 0.235 4491 Planarity : 0.004 0.036 4803 Dihedral : 3.934 23.492 5118 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.98 % Allowed : 8.33 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 3717 helix: 2.34 (0.21), residues: 645 sheet: 1.32 (0.16), residues: 1026 loop : -0.21 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.004 0.001 HIS A 655 PHE 0.017 0.001 PHE F 65 TYR 0.018 0.001 TYR A1067 ARG 0.007 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 245 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7843 (tt0) cc_final: 0.7366 (tt0) REVERT: C 305 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.7109 (p) REVERT: C 979 ASP cc_start: 0.6675 (m-30) cc_final: 0.6458 (m-30) REVERT: C 1038 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7446 (mmtm) REVERT: F 562 PHE cc_start: 0.6411 (p90) cc_final: 0.6206 (p90) REVERT: F 567 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6431 (mtm110) outliers start: 60 outliers final: 36 residues processed: 272 average time/residue: 1.2974 time to fit residues: 431.8129 Evaluate side-chains 268 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 1.9990 chunk 205 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1002 GLN C1005 GLN C1010 GLN F 607 GLN F1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26445 Z= 0.266 Angle : 0.549 7.112 36312 Z= 0.286 Chirality : 0.047 0.272 4491 Planarity : 0.004 0.042 4803 Dihedral : 4.121 23.680 5118 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.37 % Allowed : 8.53 % Favored : 88.10 % 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: 0.87 (0.13), residues: 3717 helix: 2.16 (0.20), residues: 645 sheet: 1.26 (0.15), residues: 1020 loop : -0.28 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1102 HIS 0.006 0.001 HIS C1058 PHE 0.019 0.002 PHE F 643 TYR 0.023 0.002 TYR A1067 ARG 0.009 0.001 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 232 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7941 (tt0) cc_final: 0.7494 (tt0) REVERT: C 305 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.7186 (p) REVERT: F 562 PHE cc_start: 0.6537 (p90) cc_final: 0.6294 (p90) outliers start: 68 outliers final: 48 residues processed: 272 average time/residue: 1.1549 time to fit residues: 376.6747 Evaluate side-chains 271 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 30.0000 chunk 326 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 362 optimal weight: 0.0040 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 50.0000 chunk 190 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C 52 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1005 GLN C1010 GLN F 607 GLN F1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26445 Z= 0.194 Angle : 0.519 8.017 36312 Z= 0.267 Chirality : 0.046 0.242 4491 Planarity : 0.004 0.046 4803 Dihedral : 4.121 23.179 5118 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.98 % Allowed : 9.52 % Favored : 87.50 % 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: 0.93 (0.13), residues: 3717 helix: 2.34 (0.21), residues: 645 sheet: 1.24 (0.15), residues: 1020 loop : -0.26 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 PHE 0.020 0.002 PHE F 643 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.000 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7884 (tt0) cc_final: 0.7333 (tt0) REVERT: C 305 SER cc_start: 0.7451 (OUTLIER) cc_final: 0.7197 (p) outliers start: 60 outliers final: 44 residues processed: 266 average time/residue: 1.1844 time to fit residues: 377.4884 Evaluate side-chains 273 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 305 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 361 optimal weight: 30.0000 chunk 226 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1005 GLN C 52 GLN C 607 GLN C1005 GLN C1010 GLN F 607 GLN F 935 GLN F 955 ASN F1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26445 Z= 0.219 Angle : 0.535 9.799 36312 Z= 0.276 Chirality : 0.046 0.245 4491 Planarity : 0.004 0.039 4803 Dihedral : 4.140 23.264 5118 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 9.47 % Favored : 87.20 % 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: 0.87 (0.13), residues: 3717 helix: 2.31 (0.20), residues: 645 sheet: 1.18 (0.16), residues: 1023 loop : -0.29 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS C1058 PHE 0.024 0.002 PHE F 392 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 244 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7933 (tt0) cc_final: 0.7387 (tt0) REVERT: C 305 SER cc_start: 0.7500 (OUTLIER) cc_final: 0.7259 (p) REVERT: F 780 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: F 935 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.5896 (tt0) outliers start: 67 outliers final: 47 residues processed: 283 average time/residue: 1.1989 time to fit residues: 404.3853 Evaluate side-chains 281 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 935 GLN Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 108 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 229 optimal weight: 40.0000 chunk 246 optimal weight: 50.0000 chunk 178 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 284 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1005 GLN C 52 GLN C 607 GLN C1005 GLN C1010 GLN F 607 GLN F1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26445 Z= 0.219 Angle : 0.529 8.136 36312 Z= 0.273 Chirality : 0.046 0.244 4491 Planarity : 0.004 0.039 4803 Dihedral : 4.129 25.118 5118 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.03 % Allowed : 10.02 % Favored : 86.95 % 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: 0.83 (0.14), residues: 3717 helix: 2.26 (0.21), residues: 651 sheet: 1.14 (0.16), residues: 1023 loop : -0.32 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.004 0.001 HIS C1058 PHE 0.024 0.002 PHE A 643 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG F 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 233 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7921 (tt0) cc_final: 0.7375 (tt0) REVERT: C 305 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7252 (p) REVERT: F 780 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7408 (tp30) outliers start: 61 outliers final: 49 residues processed: 272 average time/residue: 1.1601 time to fit residues: 377.6538 Evaluate side-chains 283 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 232 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.1980 chunk 346 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 336 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 304 optimal weight: 0.5980 chunk 318 optimal weight: 0.7980 chunk 335 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C 52 GLN C 607 GLN C1010 GLN F 607 GLN F1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26445 Z= 0.175 Angle : 0.511 8.105 36312 Z= 0.263 Chirality : 0.045 0.241 4491 Planarity : 0.004 0.042 4803 Dihedral : 3.972 24.895 5118 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.68 % Allowed : 10.52 % Favored : 86.81 % 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: 0.91 (0.14), residues: 3717 helix: 2.39 (0.21), residues: 651 sheet: 1.15 (0.16), residues: 1017 loop : -0.26 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 PHE 0.021 0.002 PHE F 65 TYR 0.018 0.001 TYR F1067 ARG 0.008 0.000 ARG F 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 229 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7908 (tt0) cc_final: 0.7368 (tt0) REVERT: F 780 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7329 (tp30) outliers start: 54 outliers final: 48 residues processed: 262 average time/residue: 1.1881 time to fit residues: 371.4720 Evaluate side-chains 274 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 chunk 217 optimal weight: 0.3980 chunk 168 optimal weight: 7.9990 chunk 247 optimal weight: 40.0000 chunk 373 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 297 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 229 optimal weight: 50.0000 chunk 182 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN A 804 GLN A1002 GLN A1005 GLN A1135 ASN C 52 GLN C 607 GLN C1010 GLN C1135 ASN F 607 GLN F1002 GLN F1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 26445 Z= 0.465 Angle : 0.685 12.287 36312 Z= 0.357 Chirality : 0.052 0.261 4491 Planarity : 0.005 0.045 4803 Dihedral : 4.907 49.456 5118 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.83 % Allowed : 10.66 % Favored : 86.51 % 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: 0.38 (0.13), residues: 3717 helix: 1.55 (0.20), residues: 654 sheet: 0.92 (0.16), residues: 1017 loop : -0.52 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F1102 HIS 0.009 0.002 HIS A1058 PHE 0.031 0.003 PHE F 643 TYR 0.027 0.003 TYR A1067 ARG 0.006 0.001 ARG F1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 237 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 44 residues processed: 278 average time/residue: 1.2134 time to fit residues: 402.1251 Evaluate side-chains 274 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 780 GLU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 810 SER Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 902 MET Chi-restraints excluded: chain F residue 988 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 20.0000 chunk 316 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 274 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 124 optimal weight: 50.0000 chunk 305 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A1005 GLN C 607 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 314 GLN F 607 GLN F 644 GLN F1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.226590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.176821 restraints weight = 28071.206| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 5.62 r_work: 0.3209 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26445 Z= 0.239 Angle : 0.558 12.288 36312 Z= 0.289 Chirality : 0.047 0.246 4491 Planarity : 0.004 0.050 4803 Dihedral : 4.764 68.539 5118 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.38 % Allowed : 11.41 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3717 helix: 2.01 (0.20), residues: 651 sheet: 0.94 (0.16), residues: 1017 loop : -0.42 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS A1058 PHE 0.023 0.002 PHE A 392 TYR 0.026 0.002 TYR C 380 ARG 0.008 0.000 ARG F 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8009.52 seconds wall clock time: 144 minutes 50.67 seconds (8690.67 seconds total)