Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 12:23:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/07_2023/7soe_25268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/07_2023/7soe_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_25268/07_2023/7soe_25268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/07_2023/7soe_25268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/07_2023/7soe_25268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soe_25268/07_2023/7soe_25268.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 17 Time building chain proxies: 12.38, per 1000 atoms: 0.48 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: 10.51 Conformation dependent library (CDL) restraints added in 4.3 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: 2.13 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: 13.96 Time building geometry restraints manager: 11.29 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: 14772 17.50 - 34.99: 366 34.99 - 52.49: 60 52.49 - 69.99: 42 69.99 - 87.48: 18 Dihedral angle restraints: 15258 sinusoidal: 4350 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 15255 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: 6.490 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: 0.010 Extract box with map and model: 28.630 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 69.650 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.230 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.600 ------------------------------------------------------------------------------- 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 : 9.882 87.485 8049 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 % 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 *********************** 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 : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 401 average time/residue: 1.1791 time to fit residues: 556.9508 Evaluate side-chains 265 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3503 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 26445 Z= 0.226 Angle : 0.569 8.017 36312 Z= 0.307 Chirality : 0.047 0.201 4491 Planarity : 0.005 0.036 4803 Dihedral : 4.167 17.950 3921 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 3.17 % 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: 0.90 (0.13), residues: 3717 helix: 1.93 (0.20), residues: 648 sheet: 1.27 (0.16), residues: 984 loop : -0.13 (0.13), residues: 2085 *********************** 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 346 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 282 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 306 average time/residue: 1.1931 time to fit residues: 434.0665 Evaluate side-chains 277 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 240 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 17 residues processed: 20 average time/residue: 1.0155 time to fit residues: 27.8264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 283 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 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: 0.9990 chunk 116 optimal weight: 40.0000 chunk 273 optimal weight: 0.0010 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 A1002 GLN A1005 GLN C 314 GLN C 607 GLN C 613 GLN C 658 ASN C1002 GLN C1005 GLN C1010 GLN F 314 GLN F 613 GLN F 644 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 26445 Z= 0.293 Angle : 0.584 8.096 36312 Z= 0.308 Chirality : 0.048 0.241 4491 Planarity : 0.004 0.039 4803 Dihedral : 4.105 16.995 3921 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 3.87 % 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: 0.70 (0.13), residues: 3717 helix: 1.86 (0.20), residues: 645 sheet: 1.18 (0.15), residues: 1020 loop : -0.36 (0.13), residues: 2052 *********************** 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 331 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 253 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 36 residues processed: 290 average time/residue: 1.1032 time to fit residues: 384.3413 Evaluate side-chains 273 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 18 residues processed: 18 average time/residue: 0.8023 time to fit residues: 22.0598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 177 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 229 optimal weight: 50.0000 chunk 342 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 607 GLN C 804 GLN C 935 GLN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN F1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 26445 Z= 0.259 Angle : 0.554 8.071 36312 Z= 0.289 Chirality : 0.047 0.218 4491 Planarity : 0.004 0.039 4803 Dihedral : 3.957 17.484 3921 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 3717 helix: 2.01 (0.20), residues: 645 sheet: 1.13 (0.15), residues: 1020 loop : -0.39 (0.13), residues: 2052 *********************** 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 317 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 246 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 46 residues processed: 285 average time/residue: 1.1891 time to fit residues: 403.7817 Evaluate side-chains 281 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 29 residues processed: 17 average time/residue: 0.7773 time to fit residues: 20.5000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 935 GLN A1002 GLN A1005 GLN C 52 GLN C 607 GLN C 658 ASN C1002 GLN C1005 GLN C1010 GLN F 607 GLN F 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 26445 Z= 0.251 Angle : 0.558 11.452 36312 Z= 0.286 Chirality : 0.047 0.187 4491 Planarity : 0.004 0.039 4803 Dihedral : 3.917 18.867 3921 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 3717 helix: 2.09 (0.20), residues: 645 sheet: 1.11 (0.15), residues: 1020 loop : -0.42 (0.13), residues: 2052 *********************** 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 316 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 246 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 282 average time/residue: 1.1695 time to fit residues: 394.5774 Evaluate side-chains 276 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 2.965 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 12 average time/residue: 0.8173 time to fit residues: 16.3029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 362 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 50.0000 chunk 190 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 935 GLN A 955 ASN C 52 GLN C 607 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 26445 Z= 0.216 Angle : 0.542 11.610 36312 Z= 0.277 Chirality : 0.047 0.288 4491 Planarity : 0.004 0.040 4803 Dihedral : 3.786 18.964 3921 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 3717 helix: 2.17 (0.21), residues: 651 sheet: 1.09 (0.16), residues: 1020 loop : -0.39 (0.13), residues: 2046 *********************** 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 299 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 277 average time/residue: 1.1472 time to fit residues: 379.8173 Evaluate side-chains 273 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 31 residues processed: 10 average time/residue: 0.9232 time to fit residues: 15.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 305 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 935 GLN A1002 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 607 GLN C 658 ASN C1005 GLN C1010 GLN F 580 GLN F 607 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 26445 Z= 0.221 Angle : 0.534 7.400 36312 Z= 0.276 Chirality : 0.046 0.216 4491 Planarity : 0.004 0.038 4803 Dihedral : 3.729 16.813 3921 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 3.03 % 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: 0.72 (0.14), residues: 3717 helix: 2.19 (0.21), residues: 651 sheet: 1.07 (0.16), residues: 1014 loop : -0.38 (0.13), residues: 2052 *********************** 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 304 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 243 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 45 residues processed: 281 average time/residue: 1.1480 time to fit residues: 386.6635 Evaluate side-chains 278 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 233 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 14 average time/residue: 1.0240 time to fit residues: 21.2608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 108 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 229 optimal weight: 40.0000 chunk 246 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 284 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 607 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN F 644 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 26445 Z= 0.186 Angle : 0.511 7.307 36312 Z= 0.263 Chirality : 0.046 0.199 4491 Planarity : 0.004 0.041 4803 Dihedral : 3.630 16.582 3921 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.28 % 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: 0.78 (0.14), residues: 3717 helix: 2.31 (0.21), residues: 651 sheet: 1.06 (0.16), residues: 1017 loop : -0.35 (0.13), residues: 2049 *********************** 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 286 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 274 average time/residue: 1.1515 time to fit residues: 377.6575 Evaluate side-chains 271 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 237 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 6 average time/residue: 0.3885 time to fit residues: 7.1529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 315 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 103 optimal weight: 0.0270 chunk 304 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 335 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 955 ASN A1002 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C1005 GLN C1010 GLN F 607 GLN F 779 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.080 26445 Z= 0.161 Angle : 0.505 11.460 36312 Z= 0.257 Chirality : 0.045 0.279 4491 Planarity : 0.004 0.042 4803 Dihedral : 3.505 17.499 3921 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.18 % 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: 2.38 (0.21), residues: 657 sheet: 1.12 (0.16), residues: 1017 loop : -0.24 (0.13), residues: 2043 *********************** 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 287 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 32 residues processed: 275 average time/residue: 1.1849 time to fit residues: 390.4790 Evaluate side-chains 268 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 3.069 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 4 average time/residue: 0.7107 time to fit residues: 7.5189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.0060 chunk 356 optimal weight: 9.9990 chunk 217 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 247 optimal weight: 40.0000 chunk 373 optimal weight: 8.9990 chunk 343 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 229 optimal weight: 50.0000 chunk 182 optimal weight: 0.9980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 779 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 607 GLN F 644 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 26445 Z= 0.275 Angle : 0.577 13.246 36312 Z= 0.296 Chirality : 0.048 0.309 4491 Planarity : 0.004 0.041 4803 Dihedral : 3.781 18.344 3921 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.88 % 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: 0.72 (0.14), residues: 3717 helix: 2.03 (0.20), residues: 660 sheet: 1.04 (0.16), residues: 1017 loop : -0.32 (0.13), residues: 2040 ********************** 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 284 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 30 residues processed: 277 average time/residue: 1.1873 time to fit residues: 392.0443 Evaluate side-chains 269 residues out of total 3309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 3 average time/residue: 0.9256 time to fit residues: 7.4815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 30.0000 chunk 316 optimal weight: 0.0010 chunk 91 optimal weight: 0.5980 chunk 274 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 124 optimal weight: 50.0000 chunk 305 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 607 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN F 314 GLN F 607 GLN F 644 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.229124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.179368 restraints weight = 28266.179| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 5.63 r_work: 0.3282 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 26445 Z= 0.139 Angle : 0.506 13.525 36312 Z= 0.255 Chirality : 0.045 0.289 4491 Planarity : 0.004 0.041 4803 Dihedral : 3.457 19.837 3921 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.88 % 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: 0.96 (0.14), residues: 3717 helix: 2.41 (0.21), residues: 657 sheet: 1.14 (0.16), residues: 1017 loop : -0.19 (0.14), residues: 2043 =============================================================================== Job complete usr+sys time: 7623.54 seconds wall clock time: 136 minutes 35.60 seconds (8195.60 seconds total)