Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:51:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8o_24320/12_2022/7r8o_24320_neut.pdb" } resolution = 3.5 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= 0.021 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 578": "OD1" <-> "OD2" Residue "E GLU 661": "OE1" <-> "OE2" Residue "E GLU 702": "OE1" <-> "OE2" Residue "E GLU 725": "OE1" <-> "OE2" Residue "E GLU 773": "OE1" <-> "OE2" Residue "E GLU 780": "OE1" <-> "OE2" Residue "E PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 868": "OE1" <-> "OE2" Residue "E TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 918": "OE1" <-> "OE2" Residue "E ASP 979": "OD1" <-> "OD2" Residue "E GLU 988": "OE1" <-> "OE2" Residue "E GLU 990": "OE1" <-> "OE2" Residue "E PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1111": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 34": "OD1" <-> "OD2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ASP 82": "OD1" <-> "OD2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P ASP 82": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 29964 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "N" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 18.57, per 1000 atoms: 0.62 Number of scatterers: 29964 At special positions: 0 Unit cell: (141.647, 139.909, 193.787, 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 141 16.00 O 5820 8.00 N 4941 7.00 C 19062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.01 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.05 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " 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 Atom "HETATM29962 O5 NAG E1310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG Q 1 " - " FUC Q 5 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 343 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 282 " " NAG E1305 " - " ASN E 616 " " NAG E1306 " - " ASN E 657 " " NAG E1307 " - " ASN E 717 " " NAG E1308 " - " ASN E 801 " " NAG E1309 " - " ASN E1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG Q 1 " - " ASN E 343 " Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 5.0 seconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 63 sheets defined 22.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.806A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.141A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.027A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.424A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.806A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.142A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.027A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.427A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.805A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.336A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 616 through 620 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.141A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 4.027A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.825A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU N 83 " --> pdb=" O GLU N 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU P 83 " --> pdb=" O GLU P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.118A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.280A pdb=" N PHE A 43 " --> pdb=" O ARG E 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.592A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.915A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.211A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.486A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.127A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.753A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 719 through 728 removed outlier: 3.565A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.185A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.117A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.591A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.915A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.211A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.128A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.622A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.565A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.117A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.592A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP E 104 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 127 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.914A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR E 612 " --> pdb=" O CYS E 649 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.127A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AE9, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.566A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'E' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AF6, first strand: chain 'H' and resid 56 through 59 removed outlier: 4.136A pdb=" N THR H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE H 52 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.599A pdb=" N ALA L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY L 89 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL L 33 " --> pdb=" O ARG L 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AG2, first strand: chain 'M' and resid 56 through 59 removed outlier: 4.135A pdb=" N THR M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE M 52 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN M 39 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.589A pdb=" N ALA N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY N 89 " --> pdb=" O ASP N 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL N 33 " --> pdb=" O ARG N 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG5, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AG6, first strand: chain 'O' and resid 18 through 20 Processing sheet with id=AG7, first strand: chain 'O' and resid 56 through 59 removed outlier: 4.135A pdb=" N THR O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE O 52 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE O 34 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN O 39 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 9 through 11 removed outlier: 3.602A pdb=" N ALA P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY P 89 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL P 33 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP P 35 " --> pdb=" O VAL P 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 19 through 24 removed outlier: 3.554A pdb=" N ILE P 75 " --> pdb=" O VAL P 19 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3081 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: 15.03 Time building geometry restraints manager: 13.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8368 1.33 - 1.46: 8471 1.46 - 1.59: 13614 1.59 - 1.72: 9 1.72 - 1.85: 183 Bond restraints: 30645 Sorted by residual: bond pdb=" C VAL P 19 " pdb=" CA AVAL P 19 " ideal model delta sigma weight residual 1.524 1.267 0.257 1.14e-02 7.69e+03 5.07e+02 bond pdb=" C VAL P 19 " pdb=" CA BVAL P 19 " ideal model delta sigma weight residual 1.524 1.267 0.257 1.14e-02 7.69e+03 5.07e+02 bond pdb=" N PRO A 812 " pdb=" CD PRO A 812 " ideal model delta sigma weight residual 1.473 1.290 0.183 1.40e-02 5.10e+03 1.70e+02 bond pdb=" C VAL N 19 " pdb=" CA AVAL N 19 " ideal model delta sigma weight residual 1.524 1.384 0.141 1.19e-02 7.06e+03 1.39e+02 bond pdb=" C VAL N 19 " pdb=" CA BVAL N 19 " ideal model delta sigma weight residual 1.524 1.384 0.141 1.19e-02 7.06e+03 1.39e+02 ... (remaining 30640 not shown) Histogram of bond angle deviations from ideal: 95.67 - 104.40: 614 104.40 - 113.13: 15965 113.13 - 121.86: 18199 121.86 - 130.59: 6836 130.59 - 139.32: 92 Bond angle restraints: 41706 Sorted by residual: angle pdb=" O VAL N 19 " pdb=" C VAL N 19 " pdb=" CA AVAL N 19 " ideal model delta sigma weight residual 120.51 134.33 -13.82 1.05e+00 9.07e-01 1.73e+02 angle pdb=" O VAL N 19 " pdb=" C VAL N 19 " pdb=" CA BVAL N 19 " ideal model delta sigma weight residual 120.51 134.33 -13.82 1.05e+00 9.07e-01 1.73e+02 angle pdb=" CA AVAL N 19 " pdb=" C VAL N 19 " pdb=" N THR N 20 " ideal model delta sigma weight residual 116.70 102.86 13.84 1.10e+00 8.26e-01 1.58e+02 angle pdb=" CA BVAL N 19 " pdb=" C VAL N 19 " pdb=" N THR N 20 " ideal model delta sigma weight residual 116.70 102.86 13.84 1.10e+00 8.26e-01 1.58e+02 angle pdb=" CA ARG B 214 " pdb=" CB ARG B 214 " pdb=" CG ARG B 214 " ideal model delta sigma weight residual 114.10 134.71 -20.61 2.00e+00 2.50e-01 1.06e+02 ... (remaining 41701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16871 17.99 - 35.97: 938 35.97 - 53.96: 217 53.96 - 71.95: 53 71.95 - 89.93: 41 Dihedral angle restraints: 18120 sinusoidal: 7128 harmonic: 10992 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.52 -80.48 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.53 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.55 -80.45 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 18117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 4766 0.282 - 0.564: 56 0.564 - 0.846: 5 0.846 - 1.128: 0 1.128 - 1.410: 1 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.14e+02 chirality pdb=" C1 FUC Q 5 " pdb=" O6 NAG Q 1 " pdb=" C2 FUC Q 5 " pdb=" O5 FUC Q 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.00e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.40e+02 ... (remaining 4825 not shown) Planarity restraints: 5378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E1098 " 0.367 2.00e-02 2.50e+03 3.43e-01 1.47e+03 pdb=" CG ASN E1098 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN E1098 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN E1098 " -0.578 2.00e-02 2.50e+03 pdb=" C1 NAG E1309 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.295 2.00e-02 2.50e+03 2.53e-01 7.99e+02 pdb=" C7 NAG A1304 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.277 2.00e-02 2.50e+03 2.38e-01 7.06e+02 pdb=" C7 NAG F 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.039 2.00e-02 2.50e+03 ... (remaining 5375 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 122 2.48 - 3.09: 20065 3.09 - 3.69: 44284 3.69 - 4.30: 64667 4.30 - 4.90: 107191 Nonbonded interactions: 236329 Sorted by model distance: nonbonded pdb=" O GLN E 804 " pdb=" CD PRO E 817 " model vdw 1.876 3.440 nonbonded pdb=" O GLN B 804 " pdb=" CD PRO B 817 " model vdw 1.888 3.440 nonbonded pdb=" O ASP A1127 " pdb=" OD1 ASP A1127 " model vdw 1.908 3.040 nonbonded pdb=" ND2 ASN E1134 " pdb=" O5 NAG E1310 " model vdw 1.909 2.520 nonbonded pdb=" O GLN A 804 " pdb=" CD PRO A 817 " model vdw 1.983 3.440 ... (remaining 236324 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 'E' and (resid 15 through 1140 or resid 1301 through 1308)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and (resid 2 through 18 or resid 20 through 106)) selection = (chain 'N' and (resid 2 through 18 or resid 20 through 106)) selection = (chain 'P' and (resid 2 through 18 or resid 20 through 106)) } 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 141 5.16 5 C 19062 2.51 5 N 4941 2.21 5 O 5820 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.960 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.260 Process input model: 84.440 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.257 30645 Z= 0.522 Angle : 1.476 23.020 41706 Z= 0.905 Chirality : 0.088 1.410 4828 Planarity : 0.016 0.253 5346 Dihedral : 12.774 89.935 10950 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 3747 helix: -0.04 (0.17), residues: 684 sheet: 1.01 (0.16), residues: 873 loop : -0.69 (0.12), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 616 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 632 average time/residue: 0.3854 time to fit residues: 397.1398 Evaluate side-chains 407 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 400 time to evaluate : 3.613 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2550 time to fit residues: 8.3529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 955 ASN A 957 GLN A1005 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 777 ASN B 957 GLN B 969 ASN B1005 GLN B1135 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN E 804 GLN E 957 GLN E1005 GLN E1134 ASN L 6 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 37 GLN P 6 GLN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 30645 Z= 0.243 Angle : 0.664 12.876 41706 Z= 0.359 Chirality : 0.048 0.515 4828 Planarity : 0.006 0.071 5346 Dihedral : 4.878 21.661 4404 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 3747 helix: 1.75 (0.20), residues: 663 sheet: 1.05 (0.17), residues: 867 loop : -0.73 (0.12), residues: 2217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 398 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 431 average time/residue: 0.3831 time to fit residues: 273.0159 Evaluate side-chains 363 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 337 time to evaluate : 3.438 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2755 time to fit residues: 17.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 GLN E1134 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 30645 Z= 0.250 Angle : 0.590 10.586 41706 Z= 0.313 Chirality : 0.046 0.413 4828 Planarity : 0.005 0.066 5346 Dihedral : 4.646 19.689 4404 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 3747 helix: 2.19 (0.20), residues: 663 sheet: 0.81 (0.16), residues: 861 loop : -0.76 (0.12), residues: 2223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 395 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 419 average time/residue: 0.3894 time to fit residues: 267.4076 Evaluate side-chains 360 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 339 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2599 time to fit residues: 15.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 365 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 327 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN E 188 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1134 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 30645 Z= 0.415 Angle : 0.661 12.787 41706 Z= 0.348 Chirality : 0.048 0.363 4828 Planarity : 0.005 0.056 5346 Dihedral : 4.911 25.555 4404 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -0.08 (0.13), residues: 3747 helix: 2.06 (0.20), residues: 663 sheet: 0.49 (0.16), residues: 918 loop : -1.01 (0.13), residues: 2166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 371 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 38 residues processed: 415 average time/residue: 0.4101 time to fit residues: 275.7520 Evaluate side-chains 367 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 329 time to evaluate : 3.446 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.2615 time to fit residues: 23.7968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 327 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 804 GLN A1135 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 30645 Z= 0.183 Angle : 0.563 9.681 41706 Z= 0.295 Chirality : 0.045 0.294 4828 Planarity : 0.004 0.045 5346 Dihedral : 4.569 21.351 4404 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3747 helix: 2.27 (0.20), residues: 666 sheet: 0.56 (0.16), residues: 933 loop : -0.92 (0.13), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 356 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 379 average time/residue: 0.4132 time to fit residues: 255.4344 Evaluate side-chains 333 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 323 time to evaluate : 3.618 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2761 time to fit residues: 10.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 0.6980 chunk 329 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 365 optimal weight: 6.9990 chunk 303 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 188 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 804 GLN B1005 GLN ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30645 Z= 0.184 Angle : 0.540 8.824 41706 Z= 0.282 Chirality : 0.044 0.277 4828 Planarity : 0.004 0.043 5346 Dihedral : 4.422 22.257 4404 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3747 helix: 2.34 (0.20), residues: 666 sheet: 0.51 (0.16), residues: 936 loop : -0.86 (0.13), residues: 2145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 359 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 387 average time/residue: 0.4074 time to fit residues: 256.4416 Evaluate side-chains 348 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 336 time to evaluate : 3.557 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2915 time to fit residues: 11.0409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 9.9990 chunk 41 optimal weight: 0.0030 chunk 208 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 307 optimal weight: 0.8980 chunk 204 optimal weight: 0.0040 chunk 364 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30645 Z= 0.195 Angle : 0.540 9.053 41706 Z= 0.282 Chirality : 0.044 0.267 4828 Planarity : 0.004 0.043 5346 Dihedral : 4.371 20.803 4404 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3747 helix: 2.33 (0.21), residues: 666 sheet: 0.54 (0.16), residues: 933 loop : -0.83 (0.13), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 350 time to evaluate : 3.477 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: 25 outliers final: 10 residues processed: 371 average time/residue: 0.4280 time to fit residues: 254.1982 Evaluate side-chains 346 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 336 time to evaluate : 3.719 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2631 time to fit residues: 10.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0919 > 50: distance: 31 - 35: 10.758 distance: 35 - 36: 22.272 distance: 36 - 37: 25.889 distance: 37 - 38: 30.743 distance: 37 - 39: 17.970 distance: 39 - 40: 22.667 distance: 40 - 41: 26.953 distance: 40 - 43: 16.059 distance: 41 - 42: 43.241 distance: 41 - 46: 28.631 distance: 43 - 44: 28.623 distance: 43 - 45: 23.444 distance: 46 - 47: 18.412 distance: 47 - 48: 19.774 distance: 47 - 50: 8.987 distance: 48 - 49: 30.579 distance: 50 - 51: 19.565 distance: 52 - 53: 12.795 distance: 52 - 58: 28.087 distance: 53 - 54: 7.785 distance: 53 - 56: 11.458 distance: 54 - 55: 12.862 distance: 54 - 59: 13.476 distance: 56 - 57: 15.456 distance: 57 - 58: 15.920 distance: 59 - 60: 22.765 distance: 60 - 61: 20.666 distance: 60 - 63: 21.651 distance: 61 - 62: 36.207 distance: 61 - 66: 45.526 distance: 63 - 64: 34.370 distance: 63 - 65: 22.120 distance: 66 - 67: 10.887 distance: 67 - 68: 18.546 distance: 67 - 70: 16.306 distance: 68 - 69: 12.452 distance: 68 - 75: 10.380 distance: 69 - 91: 11.294 distance: 70 - 71: 10.724 distance: 71 - 72: 11.630 distance: 72 - 73: 21.107 distance: 73 - 74: 15.278 distance: 75 - 76: 11.961 distance: 76 - 77: 12.620 distance: 76 - 79: 8.676 distance: 77 - 78: 11.111 distance: 77 - 83: 11.166 distance: 79 - 80: 13.876 distance: 80 - 81: 15.894 distance: 80 - 82: 15.903 distance: 83 - 84: 8.476 distance: 84 - 85: 15.582 distance: 84 - 87: 15.318 distance: 85 - 86: 23.044 distance: 85 - 91: 22.070 distance: 87 - 88: 14.129 distance: 88 - 89: 3.698 distance: 88 - 90: 6.519 distance: 92 - 93: 10.220 distance: 92 - 95: 11.249 distance: 93 - 94: 12.798 distance: 93 - 99: 15.074 distance: 95 - 96: 16.890 distance: 96 - 97: 13.512 distance: 96 - 98: 12.873 distance: 99 - 100: 26.655 distance: 100 - 101: 36.601 distance: 100 - 103: 29.649 distance: 101 - 102: 38.773 distance: 101 - 107: 21.586 distance: 103 - 104: 11.265 distance: 104 - 105: 21.563 distance: 104 - 106: 24.568