Starting phenix.real_space_refine (version: dev) on Sun Feb 26 22:47:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k90_22737/02_2023/7k90_22737_neut.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 102": "OD1" <-> "OD2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O GLU 85": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 102": "OD1" <-> "OD2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 85": "OD1" <-> "OD2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 27": "OD1" <-> "OD2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28863 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7664 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.45, per 1000 atoms: 0.54 Number of scatterers: 28863 At special positions: 0 Unit cell: (130.35, 130.35, 196.394, 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 5652 8.00 N 4758 7.00 C 18327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.86 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.86 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.87 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 11.22 Conformation dependent library (CDL) restraints added in 4.7 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6882 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 64 sheets defined 20.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.713A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.580A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 removed outlier: 3.884A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.712A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.580A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 772 through 783 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 874 Processing helix chain 'B' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 removed outlier: 3.884A pdb=" N GLY B 910 " --> pdb=" O ASN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.712A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 removed outlier: 3.731A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.581A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.668A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 874 Processing helix chain 'C' and resid 875 through 884 removed outlier: 3.541A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.895A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.973A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.885A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.665A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.699A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.560A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 3.713A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.412A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100 through 100D removed outlier: 3.941A pdb=" N ASP H 100D" --> pdb=" O GLY H 100A" (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100 through 100D removed outlier: 3.536A pdb=" N ASN M 100C" --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP M 100D" --> pdb=" O GLY M 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 100 through 100D' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100 through 100D removed outlier: 3.535A pdb=" N ASN O 100C" --> pdb=" O GLU O 100 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP O 100D" --> pdb=" O GLY O 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 100D' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.524A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.306A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.030A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.524A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 51 removed outlier: 6.306A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.030A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.906A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.397A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.523A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.305A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.029A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.905A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.864A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.532A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.985A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF3, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.078A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS H 93 " --> pdb=" O TRP H 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP H 104 " --> pdb=" O CYS H 93 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG H 95 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.079A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS M 93 " --> pdb=" O TRP M 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP M 104 " --> pdb=" O CYS M 93 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG M 95 " --> pdb=" O ASP M 102 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.078A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.818A pdb=" N CYS O 93 " --> pdb=" O TRP O 104 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP O 104 " --> pdb=" O CYS O 93 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG O 95 " --> pdb=" O ASP O 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.139A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.137A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AG9, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.138A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 18 through 24 964 hydrogen bonds defined for protein. 2535 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: 13.37 Time building geometry restraints manager: 12.10 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: 4868 1.32 - 1.45: 8681 1.45 - 1.58: 15791 1.58 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 29499 Sorted by residual: bond pdb=" C ARG C 457 " pdb=" O ARG C 457 " ideal model delta sigma weight residual 1.242 1.198 0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" CA SER C 443 " pdb=" CB SER C 443 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.24e-02 6.50e+03 1.23e+01 bond pdb=" CA SER A 443 " pdb=" CB SER A 443 " ideal model delta sigma weight residual 1.530 1.486 0.043 1.24e-02 6.50e+03 1.22e+01 bond pdb=" N VAL B 539 " pdb=" CA VAL B 539 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.19e+01 bond pdb=" N VAL C 367 " pdb=" CA VAL C 367 " ideal model delta sigma weight residual 1.459 1.499 -0.041 1.25e-02 6.40e+03 1.06e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.05: 917 107.05 - 113.85: 16399 113.85 - 120.65: 11422 120.65 - 127.45: 11180 127.45 - 134.25: 243 Bond angle restraints: 40161 Sorted by residual: angle pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" O TYR A 453 " ideal model delta sigma weight residual 120.32 112.18 8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " pdb=" CG PHE C 456 " ideal model delta sigma weight residual 113.80 121.41 -7.61 1.00e+00 1.00e+00 5.79e+01 angle pdb=" O SER A 443 " pdb=" C SER A 443 " pdb=" N LYS A 444 " ideal model delta sigma weight residual 121.79 128.27 -6.48 9.80e-01 1.04e+00 4.38e+01 angle pdb=" N PRO C 491 " pdb=" CA PRO C 491 " pdb=" C PRO C 491 " ideal model delta sigma weight residual 113.53 122.71 -9.18 1.39e+00 5.18e-01 4.36e+01 angle pdb=" N PRO B 491 " pdb=" CA PRO B 491 " pdb=" C PRO B 491 " ideal model delta sigma weight residual 113.53 122.47 -8.94 1.39e+00 5.18e-01 4.14e+01 ... (remaining 40156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 16212 21.38 - 42.76: 989 42.76 - 64.13: 171 64.13 - 85.51: 36 85.51 - 106.89: 16 Dihedral angle restraints: 17424 sinusoidal: 6690 harmonic: 10734 Sorted by residual: dihedral pdb=" C PHE C 456 " pdb=" N PHE C 456 " pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " ideal model delta harmonic sigma weight residual -122.60 -145.82 23.22 0 2.50e+00 1.60e-01 8.63e+01 dihedral pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CA PHE C 456 " pdb=" CB PHE C 456 " ideal model delta harmonic sigma weight residual 122.80 145.81 -23.01 0 2.50e+00 1.60e-01 8.47e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -5.09 -80.91 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 17421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4620 0.183 - 0.366: 34 0.366 - 0.550: 3 0.550 - 0.733: 1 0.733 - 0.916: 1 Chirality restraints: 4659 Sorted by residual: chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA TYR A 453 " pdb=" N TYR A 453 " pdb=" C TYR A 453 " pdb=" CB TYR A 453 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CA TYR C 453 " pdb=" N TYR C 453 " pdb=" C TYR C 453 " pdb=" CB TYR C 453 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 ... (remaining 4656 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 489 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C TYR B 489 " -0.066 2.00e-02 2.50e+03 pdb=" O TYR B 489 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 490 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 489 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C TYR C 489 " -0.065 2.00e-02 2.50e+03 pdb=" O TYR C 489 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE C 490 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 451 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C TYR C 451 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR C 451 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 452 " -0.022 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 3 1.92 - 2.66: 638 2.66 - 3.41: 38194 3.41 - 4.15: 68316 4.15 - 4.90: 125359 Nonbonded interactions: 232510 Sorted by model distance: nonbonded pdb=" OE2 GLU H 100 " pdb=" N TYR H 100I" model vdw 1.169 2.520 nonbonded pdb=" OE2 GLU H 100 " pdb=" CA TYR H 100I" model vdw 1.368 3.470 nonbonded pdb=" NH1 ARG B 457 " pdb=" O SER B 459 " model vdw 1.855 2.520 nonbonded pdb=" O ASN C 540 " pdb=" OD1 ASN C 540 " model vdw 1.949 3.040 nonbonded pdb=" NE2 GLN B 493 " pdb=" OD1 ASN H 31 " model vdw 1.966 2.520 ... (remaining 232505 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 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18327 2.51 5 N 4758 2.21 5 O 5652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 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: 18.860 Check model and map are aligned: 0.460 Process input model: 75.840 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.004 0.061 29499 Z= 0.269 Angle : 0.709 11.320 40161 Z= 0.433 Chirality : 0.055 0.916 4659 Planarity : 0.004 0.038 5157 Dihedral : 14.345 106.891 10416 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.03 % Favored : 94.64 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.32 % 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: -4.00 (0.12), residues: 3639 helix: -4.08 (0.12), residues: 690 sheet: -2.08 (0.15), residues: 870 loop : -2.43 (0.12), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 521 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 554 average time/residue: 0.4116 time to fit residues: 361.1783 Evaluate side-chains 353 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 3.081 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2871 time to fit residues: 12.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 196 ASN A 334 ASN A 493 GLN A 607 GLN A 755 GLN A 762 GLN A 853 GLN A 901 GLN A 913 GLN A 965 GLN A1106 GLN A1135 ASN B 52 GLN B 134 GLN B 196 ASN B 207 HIS B 394 ASN B 409 GLN B 450 ASN B 580 GLN B 607 GLN B 755 GLN B 762 GLN B 774 GLN B 895 GLN B 901 GLN B 913 GLN B 949 GLN B 965 GLN B1101 HIS B1106 GLN C 52 GLN C 134 GLN C 196 ASN C 580 GLN C 607 GLN C 655 HIS C 755 GLN C 762 GLN C 779 GLN C 787 GLN C 853 GLN C 895 GLN C 901 GLN C 913 GLN C 919 ASN C 965 GLN C1101 HIS C1106 GLN H 39 GLN H 81 GLN M 31 ASN M 39 GLN O 31 ASN O 39 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 39 HIS L 53 ASN N 17 GLN N 38 GLN N 39 HIS N 53 ASN P 17 GLN P 38 GLN P 39 HIS P 53 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 29499 Z= 0.237 Angle : 0.613 10.676 40161 Z= 0.321 Chirality : 0.047 0.317 4659 Planarity : 0.004 0.039 5157 Dihedral : 6.477 106.750 4167 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.96 (0.12), residues: 3639 helix: -2.89 (0.16), residues: 681 sheet: -1.50 (0.16), residues: 873 loop : -1.83 (0.12), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 373 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 43 residues processed: 445 average time/residue: 0.3974 time to fit residues: 286.0951 Evaluate side-chains 353 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 310 time to evaluate : 3.356 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2981 time to fit residues: 27.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 267 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 394 ASN A 779 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 280 ASN B 334 ASN B 440 ASN B 764 ASN B 856 ASN C 787 GLN H 39 GLN M 31 ASN M 39 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN N 53 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 29499 Z= 0.248 Angle : 0.587 9.979 40161 Z= 0.306 Chirality : 0.047 0.303 4659 Planarity : 0.004 0.042 5157 Dihedral : 6.360 106.986 4167 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer Outliers : 2.89 % 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: -2.26 (0.13), residues: 3639 helix: -1.90 (0.18), residues: 672 sheet: -0.84 (0.18), residues: 732 loop : -1.63 (0.12), residues: 2235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 358 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 42 residues processed: 431 average time/residue: 0.4268 time to fit residues: 300.1494 Evaluate side-chains 344 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 302 time to evaluate : 3.416 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2676 time to fit residues: 25.8698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 334 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 174 optimal weight: 0.0870 chunk 316 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 388 ASN A 779 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN C 207 HIS C 334 ASN C 544 ASN P 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 29499 Z= 0.184 Angle : 0.549 9.532 40161 Z= 0.285 Chirality : 0.045 0.292 4659 Planarity : 0.004 0.044 5157 Dihedral : 6.215 107.461 4167 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer Outliers : 2.09 % 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: -1.93 (0.13), residues: 3639 helix: -1.32 (0.20), residues: 645 sheet: -0.84 (0.17), residues: 837 loop : -1.46 (0.13), residues: 2157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 33 residues processed: 375 average time/residue: 0.3886 time to fit residues: 239.3389 Evaluate side-chains 308 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 275 time to evaluate : 3.169 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2859 time to fit residues: 21.3524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 895 GLN B 121 ASN B 196 ASN B 207 HIS B 544 ASN B 779 GLN B 856 ASN C 280 ASN C 949 GLN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN N 53 ASN P 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 29499 Z= 0.381 Angle : 0.649 10.152 40161 Z= 0.336 Chirality : 0.049 0.338 4659 Planarity : 0.004 0.051 5157 Dihedral : 6.565 107.319 4167 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.27 % Favored : 93.62 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.07 (0.13), residues: 3639 helix: -1.70 (0.19), residues: 678 sheet: -0.80 (0.17), residues: 813 loop : -1.50 (0.13), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 290 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 42 residues processed: 348 average time/residue: 0.4163 time to fit residues: 235.0656 Evaluate side-chains 302 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 3.637 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2601 time to fit residues: 25.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 1.9990 chunk 318 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 354 optimal weight: 20.0000 chunk 293 optimal weight: 4.9990 chunk 163 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 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 655 HIS B 121 ASN B 207 HIS B 779 GLN C 121 ASN C 280 ASN C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN L 53 ASN P 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 29499 Z= 0.198 Angle : 0.560 9.420 40161 Z= 0.290 Chirality : 0.046 0.304 4659 Planarity : 0.004 0.048 5157 Dihedral : 6.309 107.990 4167 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.47 % Rotamer Outliers : 1.25 % 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: -1.80 (0.13), residues: 3639 helix: -1.35 (0.19), residues: 690 sheet: -0.75 (0.17), residues: 840 loop : -1.30 (0.13), residues: 2109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 280 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 310 average time/residue: 0.4013 time to fit residues: 204.5548 Evaluate side-chains 275 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2840 time to fit residues: 16.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 8.9990 chunk 39 optimal weight: 0.1980 chunk 201 optimal weight: 0.6980 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 856 ASN C 280 ASN C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN O 39 GLN ** O 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN P 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 29499 Z= 0.174 Angle : 0.540 9.314 40161 Z= 0.279 Chirality : 0.045 0.294 4659 Planarity : 0.004 0.047 5157 Dihedral : 6.173 108.063 4167 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.86 % Favored : 95.03 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3639 helix: -0.98 (0.20), residues: 663 sheet: -0.77 (0.16), residues: 903 loop : -1.21 (0.13), residues: 2073 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 286 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 311 average time/residue: 0.4124 time to fit residues: 210.3311 Evaluate side-chains 275 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2743 time to fit residues: 13.1318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 224 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN B 856 ASN B 955 ASN C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN L 53 ASN P 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 29499 Z= 0.188 Angle : 0.540 9.638 40161 Z= 0.279 Chirality : 0.045 0.297 4659 Planarity : 0.004 0.048 5157 Dihedral : 6.143 108.148 4167 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer Outliers : 0.77 % 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: -1.50 (0.13), residues: 3639 helix: -0.88 (0.20), residues: 663 sheet: -0.66 (0.16), residues: 900 loop : -1.15 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 274 time to evaluate : 3.389 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 291 average time/residue: 0.4193 time to fit residues: 198.2892 Evaluate side-chains 268 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 255 time to evaluate : 3.693 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3608 time to fit residues: 15.0048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 0.0770 chunk 310 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1010 GLN B 544 ASN B 856 ASN C 334 ASN L 53 ASN P 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 29499 Z= 0.177 Angle : 0.535 9.291 40161 Z= 0.276 Chirality : 0.045 0.298 4659 Planarity : 0.004 0.048 5157 Dihedral : 6.108 108.381 4167 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer Outliers : 0.45 % 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: -1.38 (0.13), residues: 3639 helix: -0.79 (0.20), residues: 663 sheet: -0.45 (0.17), residues: 879 loop : -1.14 (0.13), residues: 2097 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 268 time to evaluate : 3.221 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 278 average time/residue: 0.4246 time to fit residues: 193.1334 Evaluate side-chains 261 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3229 time to fit residues: 10.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 3.9990 chunk 347 optimal weight: 0.1980 chunk 212 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 493 GLN A 804 GLN A 935 GLN B 498 GLN B 856 ASN C 334 ASN C 564 GLN L 53 ASN P 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 29499 Z= 0.210 Angle : 0.551 9.306 40161 Z= 0.283 Chirality : 0.046 0.304 4659 Planarity : 0.004 0.049 5157 Dihedral : 6.146 108.449 4167 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer Outliers : 0.51 % 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: -1.39 (0.13), residues: 3639 helix: -0.85 (0.20), residues: 663 sheet: -0.38 (0.17), residues: 822 loop : -1.15 (0.13), residues: 2154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 3.327 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 268 average time/residue: 0.4526 time to fit residues: 201.6916 Evaluate side-chains 254 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 3.123 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2959 time to fit residues: 9.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 334 ASN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.190888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144452 restraints weight = 34682.770| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.78 r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 29499 Z= 0.178 Angle : 0.535 9.188 40161 Z= 0.275 Chirality : 0.045 0.303 4659 Planarity : 0.004 0.048 5157 Dihedral : 6.092 108.741 4167 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer Outliers : 0.29 % 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: -1.27 (0.13), residues: 3639 helix: -0.70 (0.20), residues: 663 sheet: -0.31 (0.17), residues: 822 loop : -1.09 (0.13), residues: 2154 =============================================================================== Job complete usr+sys time: 6034.84 seconds wall clock time: 111 minutes 51.10 seconds (6711.10 seconds total)