Starting phenix.real_space_refine (version: dev) on Sat Feb 25 16:59:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2023/6ozc_20224.pdb" } resolution = 3.79 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= 0.001 sd= 0.061 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 GLU 381": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25821 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "F" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "R" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "P" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "o" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "t" 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 14.24, per 1000 atoms: 0.55 Number of scatterers: 25821 At special positions: 0 Unit cell: (188.64, 197.81, 137.55, 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 150 16.00 O 5424 8.00 N 4164 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.07 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.12 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN W 5 " - " MAN W 6 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN c 4 " - " MAN c 5 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN g 5 " - " MAN g 6 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN m 4 " - " MAN m 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN q 5 " - " MAN q 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 5 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 7 " - " MAN e 8 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 8 " " MAN i 4 " - " MAN i 5 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 8 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 7 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 7 " " MAN e 7 " - " MAN e 9 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 7 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 7 " " BMA m 3 " - " MAN m 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 7 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 626 " - " ASN A 133 " " NAG A 653 " - " ASN A 234 " " NAG A 656 " - " ASN A 160 " " NAG A 659 " - " ASN A 197 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 626 " - " ASN E 133 " " NAG E 653 " - " ASN E 234 " " NAG E 656 " - " ASN E 160 " " NAG E 659 " - " ASN E 197 " " NAG F 626 " - " ASN F 133 " " NAG F 653 " - " ASN F 234 " " NAG F 656 " - " ASN F 160 " " NAG F 659 " - " ASN F 197 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 339 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 392 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 339 " " NAG j 1 " - " ASN E 448 " " NAG k 1 " - " ASN E 301 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN F 262 " " NAG n 1 " - " ASN F 363 " " NAG o 1 " - " ASN F 392 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 332 " " NAG r 1 " - " ASN F 295 " " NAG s 1 " - " ASN F 339 " " NAG t 1 " - " ASN F 448 " " NAG u 1 " - " ASN F 301 " " NAG v 1 " - " ASN F 156 " Time building additional restraints: 14.35 Conformation dependent library (CDL) restraints added in 3.6 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 66 sheets defined 18.1% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 4.063A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 661 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 52A through 55 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 52A through 55 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU I 592 " --> pdb=" O ARG I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 661 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 55 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 52A through 55 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 495 through 498 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.636A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.536A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 495 through 498 Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AF2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF3, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AF4, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AF5, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 358 through 361 Processing sheet with id=AF7, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 416 Processing sheet with id=AF8, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AG1, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.663A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2421 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: 10.95 Time building geometry restraints manager: 14.40 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: 5455 1.32 - 1.45: 8504 1.45 - 1.59: 12135 1.59 - 1.72: 21 1.72 - 1.86: 198 Bond restraints: 26313 Sorted by residual: bond pdb=" C THR B 627 " pdb=" N TRP B 628 " ideal model delta sigma weight residual 1.335 1.247 0.087 1.25e-02 6.40e+03 4.90e+01 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.89e+01 bond pdb=" C THR G 627 " pdb=" N TRP G 628 " ideal model delta sigma weight residual 1.335 1.247 0.087 1.25e-02 6.40e+03 4.89e+01 bond pdb=" CB TYR R 91 " pdb=" CG TYR R 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.88e+01 bond pdb=" CB TYR Q 91 " pdb=" CG TYR Q 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.87e+01 ... (remaining 26308 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.05: 855 106.05 - 113.13: 14743 113.13 - 120.20: 10030 120.20 - 127.27: 9753 127.27 - 134.34: 331 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N ARG J 66 " pdb=" CA ARG J 66 " pdb=" C ARG J 66 " ideal model delta sigma weight residual 113.88 101.37 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG C 66 " pdb=" CA ARG C 66 " pdb=" C ARG C 66 " ideal model delta sigma weight residual 113.88 101.38 12.50 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG K 66 " pdb=" CA ARG K 66 " pdb=" C ARG K 66 " ideal model delta sigma weight residual 113.88 101.40 12.48 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N HIS E 72 " pdb=" CA HIS E 72 " pdb=" C HIS E 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 angle pdb=" N HIS F 72 " pdb=" CA HIS F 72 " pdb=" C HIS F 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15267 17.99 - 35.98: 396 35.98 - 53.97: 111 53.97 - 71.97: 63 71.97 - 89.96: 21 Dihedral angle restraints: 15858 sinusoidal: 7197 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.36 -40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.35 -40.35 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.34 -40.34 1 1.00e+01 1.00e-02 2.28e+01 ... (remaining 15855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2539 0.074 - 0.148: 1338 0.148 - 0.222: 480 0.222 - 0.296: 203 0.296 - 0.371: 42 Chirality restraints: 4602 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 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 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 4599 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.42e+01 pdb=" C7 NAG Z 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.41e+01 pdb=" C7 NAG t 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG t 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG t 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG t 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.063 2.00e-02 2.50e+03 5.21e-02 3.40e+01 pdb=" C7 NAG j 1 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8160 2.82 - 3.34: 23259 3.34 - 3.86: 43967 3.86 - 4.38: 51813 4.38 - 4.90: 83268 Nonbonded interactions: 210467 Sorted by model distance: nonbonded pdb=" O4 NAG A 659 " pdb=" O6 NAG A 659 " model vdw 2.303 2.440 nonbonded pdb=" O4 NAG E 659 " pdb=" O6 NAG E 659 " model vdw 2.304 2.440 nonbonded pdb=" O4 NAG F 659 " pdb=" O6 NAG F 659 " model vdw 2.304 2.440 nonbonded pdb=" O LEU G 568 " pdb=" OG1 THR G 569 " model vdw 2.340 2.440 nonbonded pdb=" O LEU I 568 " pdb=" OG1 THR I 569 " model vdw 2.341 2.440 ... (remaining 210462 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 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'd' selection = chain 'f' selection = chain 'n' selection = chain 'p' } ncs_group { reference = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'W' and (resid 1 or resid 4 through 8)) selection = (chain 'Y' and (resid 2 or resid 5 through 9)) selection = (chain 'e' and (resid 2 or resid 5 through 9)) selection = (chain 'g' and (resid 1 or resid 4 through 8)) selection = (chain 'i' and (resid 2 or resid 5 through 9)) selection = (chain 'o' and (resid 2 or resid 5 through 9)) selection = (chain 'q' and (resid 1 or resid 4 through 8)) selection = (chain 's' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 't' selection = chain 'u' selection = chain 'v' } 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 150 5.16 5 C 16083 2.51 5 N 4164 2.21 5 O 5424 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 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: 1.980 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: 6.010 Check model and map are aligned: 0.360 Process input model: 70.340 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 0.212 26313 Z= 1.427 Angle : 1.833 12.505 35712 Z= 1.189 Chirality : 0.107 0.371 4602 Planarity : 0.009 0.052 4233 Dihedral : 10.378 89.958 10170 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.13 % Favored : 96.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2967 helix: -1.25 (0.22), residues: 393 sheet: 0.81 (0.14), residues: 1107 loop : 0.41 (0.16), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.4385 time to fit residues: 471.0291 Evaluate side-chains 325 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 590 GLN B 616 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN L 89 GLN ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN I 616 ASN ** I 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 26313 Z= 0.330 Angle : 0.760 8.422 35712 Z= 0.413 Chirality : 0.047 0.231 4602 Planarity : 0.005 0.074 4233 Dihedral : 6.527 51.538 4779 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.99 % Favored : 94.61 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2967 helix: 0.04 (0.27), residues: 372 sheet: 0.63 (0.15), residues: 1056 loop : 0.03 (0.16), residues: 1539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 382 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 36 residues processed: 425 average time/residue: 0.4625 time to fit residues: 302.3227 Evaluate side-chains 325 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 2.975 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3223 time to fit residues: 23.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 50.0000 chunk 74 optimal weight: 7.9990 chunk 270 optimal weight: 0.5980 chunk 291 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN Q 37 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN O 82AHIS ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 82AHIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 26313 Z= 0.353 Angle : 0.708 12.200 35712 Z= 0.375 Chirality : 0.045 0.197 4602 Planarity : 0.005 0.068 4233 Dihedral : 6.322 50.753 4779 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2967 helix: 0.15 (0.28), residues: 357 sheet: 0.52 (0.15), residues: 1044 loop : -0.15 (0.16), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 316 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 356 average time/residue: 0.3868 time to fit residues: 216.2885 Evaluate side-chains 297 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2834 time to fit residues: 18.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 271 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN Q 37 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 590 GLN ** I 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 26313 Z= 0.303 Angle : 0.667 10.383 35712 Z= 0.348 Chirality : 0.045 0.206 4602 Planarity : 0.004 0.062 4233 Dihedral : 6.242 52.124 4779 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.15), residues: 2967 helix: 0.41 (0.29), residues: 339 sheet: 0.27 (0.15), residues: 1056 loop : -0.30 (0.16), residues: 1572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 296 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 52 residues processed: 345 average time/residue: 0.3830 time to fit residues: 208.8386 Evaluate side-chains 308 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2705 time to fit residues: 29.0080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN B 656 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 HIS F 130 GLN F 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN I 652 GLN R 89 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 90 HIS K 82AHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 26313 Z= 0.399 Angle : 0.705 9.831 35712 Z= 0.366 Chirality : 0.045 0.230 4602 Planarity : 0.005 0.064 4233 Dihedral : 6.389 53.138 4779 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.26 (0.15), residues: 2967 helix: 0.18 (0.29), residues: 345 sheet: 0.17 (0.16), residues: 1056 loop : -0.40 (0.16), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 283 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 306 average time/residue: 0.3985 time to fit residues: 192.2218 Evaluate side-chains 266 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2740 time to fit residues: 12.2173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 HIS E 130 GLN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82AHIS ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 26313 Z= 0.322 Angle : 0.662 9.242 35712 Z= 0.343 Chirality : 0.044 0.192 4602 Planarity : 0.004 0.065 4233 Dihedral : 6.328 55.237 4779 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.33 (0.15), residues: 2967 helix: 0.28 (0.29), residues: 345 sheet: 0.09 (0.16), residues: 1020 loop : -0.46 (0.16), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 308 average time/residue: 0.4190 time to fit residues: 203.5174 Evaluate side-chains 283 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2368 time to fit residues: 16.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN B 651 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN G 656 ASN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 26313 Z= 0.345 Angle : 0.678 11.383 35712 Z= 0.350 Chirality : 0.045 0.220 4602 Planarity : 0.004 0.063 4233 Dihedral : 6.415 59.123 4779 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.63 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2967 helix: 0.34 (0.29), residues: 345 sheet: -0.00 (0.16), residues: 1020 loop : -0.56 (0.16), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 295 average time/residue: 0.3820 time to fit residues: 178.7058 Evaluate side-chains 272 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2717 time to fit residues: 13.1200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 40.0000 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 653 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 82AHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 26313 Z= 0.444 Angle : 0.741 9.871 35712 Z= 0.385 Chirality : 0.047 0.257 4602 Planarity : 0.005 0.073 4233 Dihedral : 6.705 58.032 4779 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.02 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2967 helix: 0.08 (0.28), residues: 351 sheet: -0.17 (0.16), residues: 1053 loop : -0.70 (0.16), residues: 1563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 279 average time/residue: 0.3781 time to fit residues: 169.4226 Evaluate side-chains 273 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2455 time to fit residues: 13.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 26313 Z= 0.280 Angle : 0.664 11.437 35712 Z= 0.342 Chirality : 0.044 0.214 4602 Planarity : 0.004 0.065 4233 Dihedral : 6.471 58.153 4779 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.58 (0.15), residues: 2967 helix: 0.34 (0.29), residues: 348 sheet: -0.10 (0.16), residues: 1020 loop : -0.68 (0.16), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 274 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 280 average time/residue: 0.3843 time to fit residues: 172.0572 Evaluate side-chains 263 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 253 time to evaluate : 2.966 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2456 time to fit residues: 8.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 144 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 26313 Z= 0.293 Angle : 0.672 11.901 35712 Z= 0.344 Chirality : 0.044 0.234 4602 Planarity : 0.004 0.069 4233 Dihedral : 6.447 58.660 4779 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.07 % Favored : 93.83 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.58 (0.15), residues: 2967 helix: 0.37 (0.29), residues: 351 sheet: -0.10 (0.16), residues: 1020 loop : -0.69 (0.16), residues: 1596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 261 average time/residue: 0.3887 time to fit residues: 163.1353 Evaluate side-chains 254 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 249 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2304 time to fit residues: 6.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 58.1743 > 50: distance: 33 - 34: 10.722 distance: 34 - 35: 6.920 distance: 34 - 37: 9.173 distance: 35 - 36: 17.811 distance: 35 - 41: 7.928 distance: 37 - 38: 5.351 distance: 38 - 39: 8.060 distance: 38 - 40: 4.571 distance: 41 - 42: 7.980 distance: 42 - 43: 14.452 distance: 43 - 44: 8.934 distance: 43 - 45: 19.281 distance: 45 - 46: 21.279 distance: 46 - 47: 14.118 distance: 46 - 49: 18.038 distance: 47 - 48: 32.530 distance: 47 - 50: 14.056 distance: 50 - 51: 13.613 distance: 51 - 52: 13.032 distance: 51 - 54: 27.423 distance: 52 - 53: 40.565 distance: 52 - 55: 9.713 distance: 55 - 56: 27.573 distance: 56 - 57: 22.301 distance: 57 - 58: 17.402 distance: 57 - 59: 8.406 distance: 59 - 60: 10.547 distance: 60 - 61: 12.409 distance: 60 - 63: 5.696 distance: 61 - 62: 7.946 distance: 61 - 65: 5.016 distance: 63 - 64: 23.950 distance: 65 - 66: 5.128 distance: 66 - 67: 9.846 distance: 66 - 69: 7.018 distance: 67 - 68: 15.106 distance: 67 - 72: 10.755 distance: 69 - 70: 13.146 distance: 69 - 71: 10.202 distance: 72 - 73: 8.857 distance: 73 - 74: 11.956 distance: 73 - 76: 8.677 distance: 74 - 75: 10.895 distance: 74 - 80: 11.278 distance: 76 - 77: 6.080 distance: 77 - 78: 8.978 distance: 78 - 79: 9.174 distance: 80 - 81: 8.516 distance: 81 - 82: 8.413 distance: 82 - 83: 13.393 distance: 83 - 94: 16.500