Starting phenix.real_space_refine on Sun Nov 19 12:32:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d65_30589/11_2023/7d65_30589_updated.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 220 5.16 5 C 17303 2.51 5 N 4224 2.21 5 O 4862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 26664 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2305 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "E" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "F" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 119 Unusual residues: {'PA8': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 13.69, per 1000 atoms: 0.51 Number of scatterers: 26664 At special positions: 0 Unit cell: (158.4, 157.3, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.04 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 Time building additional restraints: 9.31 Conformation dependent library (CDL) restraints added in 4.4 seconds 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 0 sheets defined 63.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.852A pdb=" N PHE A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.508A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 4.317A pdb=" N MET A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 51 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 52 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 53 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 56 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 4.109A pdb=" N VAL A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 62 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 63 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 65 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 68 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.664A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 77' Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.882A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 172 through 203 removed outlier: 3.798A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.585A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.513A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.730A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.555A pdb=" N ALA A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.588A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 13 removed outlier: 3.902A pdb=" N PHE B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.548A pdb=" N GLY B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 4.349A pdb=" N MET B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY B 51 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 52 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 53 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 55 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.994A pdb=" N VAL B 61 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 63 " --> pdb=" O TRP B 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 65 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 68 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.741A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.913A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.590A pdb=" N TRP B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 3.525A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.586A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 246 removed outlier: 3.831A pdb=" N LEU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.563A pdb=" N ALA B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.675A pdb=" N VAL B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 removed outlier: 3.960A pdb=" N PHE C 10 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.558A pdb=" N GLY C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 68 removed outlier: 4.335A pdb=" N MET C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR C 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY C 51 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 52 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 53 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU C 55 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA C 57 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.993A pdb=" N VAL C 61 " --> pdb=" O PRO C 58 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 62 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 65 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 68 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.739A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 77' Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 109 through 120 removed outlier: 3.858A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 176 through 203 removed outlier: 3.972A pdb=" N GLN C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP C 184 " --> pdb=" O GLN C 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.646A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.595A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.601A pdb=" N VAL C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 10 through 13 No H-bonds generated for 'chain 'D' and resid 10 through 13' Processing helix chain 'D' and resid 18 through 37 removed outlier: 3.519A pdb=" N GLY D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 68 removed outlier: 4.288A pdb=" N MET D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR D 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY D 51 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 52 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 53 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 55 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 56 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA D 57 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 4.027A pdb=" N VAL D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 62 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU D 65 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 68 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.640A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.908A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 178 through 203 removed outlier: 3.504A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 192 " --> pdb=" O CYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 229 removed outlier: 3.658A pdb=" N THR D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.692A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.637A pdb=" N ALA D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.523A pdb=" N VAL D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 10 through 13 No H-bonds generated for 'chain 'E' and resid 10 through 13' Processing helix chain 'E' and resid 16 through 37 removed outlier: 3.884A pdb=" N TYR E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 68 removed outlier: 4.332A pdb=" N MET E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR E 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY E 51 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 52 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 53 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 55 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA E 57 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 4.023A pdb=" N VAL E 61 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 62 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 63 " --> pdb=" O TRP E 60 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU E 65 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE E 68 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.755A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 77' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.849A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 130 Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 172 through 175 No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 178 through 203 removed outlier: 3.505A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 192 " --> pdb=" O CYS E 188 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 229 removed outlier: 3.542A pdb=" N PHE E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 246 removed outlier: 3.926A pdb=" N ARG E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.605A pdb=" N ALA E 264 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 266 " --> pdb=" O TRP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.674A pdb=" N VAL E 284 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 10 through 13 No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 18 through 37 removed outlier: 3.501A pdb=" N GLY F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 68 removed outlier: 4.372A pdb=" N MET F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR F 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY F 51 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 52 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL F 53 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE F 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU F 55 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE F 56 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA F 57 " --> pdb=" O PHE F 54 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.978A pdb=" N VAL F 61 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 62 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 63 " --> pdb=" O TRP F 60 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 65 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE F 68 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.745A pdb=" N ARG F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 77' Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 109 through 120 removed outlier: 3.797A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 172 through 175 No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 178 through 203 removed outlier: 3.686A pdb=" N TRP F 184 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 189 " --> pdb=" O CYS F 185 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.569A pdb=" N THR F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 246 removed outlier: 3.656A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG F 240 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.664A pdb=" N ALA F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER F 266 " --> pdb=" O TRP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.536A pdb=" N VAL F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 Processing helix chain 'G' and resid 10 through 13 No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 16 through 37 removed outlier: 3.721A pdb=" N TYR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 68 removed outlier: 4.372A pdb=" N MET G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY G 51 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 52 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL G 53 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 55 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE G 56 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA G 57 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 4.043A pdb=" N VAL G 61 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU G 62 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 65 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE G 68 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 removed outlier: 3.709A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 77' Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.854A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 130 Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 167 through 170 No H-bonds generated for 'chain 'G' and resid 167 through 170' Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 178 through 203 removed outlier: 3.626A pdb=" N TRP G 184 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 229 removed outlier: 3.590A pdb=" N GLN G 220 " --> pdb=" O LYS G 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 246 removed outlier: 3.658A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG G 240 " --> pdb=" O LYS G 236 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.590A pdb=" N ALA G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER G 266 " --> pdb=" O TRP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 286 removed outlier: 3.568A pdb=" N VAL G 284 " --> pdb=" O THR G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 8 Processing helix chain 'H' and resid 10 through 13 No H-bonds generated for 'chain 'H' and resid 10 through 13' Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.528A pdb=" N GLY H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 68 removed outlier: 4.391A pdb=" N MET H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR H 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY H 51 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 52 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 53 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE H 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU H 55 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE H 56 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA H 57 " --> pdb=" O PHE H 54 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 4.084A pdb=" N VAL H 61 " --> pdb=" O PRO H 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 62 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 63 " --> pdb=" O TRP H 60 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 68 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 removed outlier: 3.791A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 77' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 109 through 120 removed outlier: 3.840A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 130 Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 167 through 170 No H-bonds generated for 'chain 'H' and resid 167 through 170' Processing helix chain 'H' and resid 172 through 175 No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 178 through 203 removed outlier: 3.508A pdb=" N LEU H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP H 184 " --> pdb=" O GLN H 180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 229 removed outlier: 3.601A pdb=" N THR H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 246 removed outlier: 3.975A pdb=" N ARG H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS H 243 " --> pdb=" O GLU H 239 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.613A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER H 266 " --> pdb=" O TRP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 286 removed outlier: 3.648A pdb=" N VAL H 284 " --> pdb=" O THR H 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 13 removed outlier: 3.891A pdb=" N PHE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 37 removed outlier: 3.552A pdb=" N GLY I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 68 removed outlier: 4.400A pdb=" N MET I 48 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR I 49 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY I 51 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU I 52 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 53 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE I 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU I 55 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE I 56 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 4.043A pdb=" N VAL I 61 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU I 62 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 63 " --> pdb=" O TRP I 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU I 65 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE I 68 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 77 No H-bonds generated for 'chain 'I' and resid 74 through 77' Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 95 through 107 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.943A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 130 Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 172 through 175 No H-bonds generated for 'chain 'I' and resid 172 through 175' Processing helix chain 'I' and resid 178 through 203 removed outlier: 3.547A pdb=" N TRP I 184 " --> pdb=" O GLN I 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER I 189 " --> pdb=" O CYS I 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE I 192 " --> pdb=" O CYS I 188 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 221 removed outlier: 3.542A pdb=" N THR I 217 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 220 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 229 Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.632A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU I 237 " --> pdb=" O TYR I 233 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 266 removed outlier: 3.608A pdb=" N ALA I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 265 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 286 removed outlier: 3.551A pdb=" N VAL I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I 285 " --> pdb=" O LEU I 281 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 286 " --> pdb=" O HIS I 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 280 through 286' Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.519A pdb=" N LEU J 8 " --> pdb=" O PHE J 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE J 10 " --> pdb=" O GLY J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 37 removed outlier: 3.548A pdb=" N GLY J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 68 removed outlier: 4.320A pdb=" N MET J 48 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR J 49 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY J 51 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL J 53 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE J 54 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 55 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA J 57 " --> pdb=" O PHE J 54 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 4.076A pdb=" N VAL J 61 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 63 " --> pdb=" O TRP J 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU J 65 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE J 68 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 77 removed outlier: 3.707A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 72 through 77' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'J' and resid 95 through 106 Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.882A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 130 Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 172 through 175 No H-bonds generated for 'chain 'J' and resid 172 through 175' Processing helix chain 'J' and resid 178 through 190 removed outlier: 3.551A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP J 184 " --> pdb=" O GLN J 180 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER J 189 " --> pdb=" O CYS J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 203 removed outlier: 3.603A pdb=" N THR J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 224 removed outlier: 3.590A pdb=" N PHE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR J 217 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN J 220 " --> pdb=" O LYS J 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 229 No H-bonds generated for 'chain 'J' and resid 226 through 229' Processing helix chain 'J' and resid 232 through 246 removed outlier: 3.650A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU J 237 " --> pdb=" O TYR J 233 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.575A pdb=" N ALA J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 286 removed outlier: 3.507A pdb=" N VAL J 284 " --> pdb=" O THR J 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL J 285 " --> pdb=" O LEU J 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 13 removed outlier: 3.893A pdb=" N PHE K 10 " --> pdb=" O GLY K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.552A pdb=" N GLY K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 68 removed outlier: 4.267A pdb=" N MET K 48 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR K 49 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY K 51 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU K 52 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 53 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU K 55 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA K 57 " --> pdb=" O PHE K 54 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.945A pdb=" N VAL K 61 " --> pdb=" O PRO K 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 63 " --> pdb=" O TRP K 60 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU K 65 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE K 68 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.736A pdb=" N ARG K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 77' Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.871A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 167 through 170 No H-bonds generated for 'chain 'K' and resid 167 through 170' Processing helix chain 'K' and resid 172 through 175 No H-bonds generated for 'chain 'K' and resid 172 through 175' Processing helix chain 'K' and resid 178 through 203 removed outlier: 3.515A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER K 189 " --> pdb=" O CYS K 185 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE K 192 " --> pdb=" O CYS K 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER K 194 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 229 removed outlier: 3.598A pdb=" N THR K 217 " --> pdb=" O SER K 213 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 246 removed outlier: 3.676A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 237 " --> pdb=" O TYR K 233 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG K 240 " --> pdb=" O LYS K 236 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 266 removed outlier: 3.555A pdb=" N ALA K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 265 " --> pdb=" O ALA K 261 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER K 266 " --> pdb=" O TRP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 286 removed outlier: 3.576A pdb=" N VAL K 284 " --> pdb=" O THR K 280 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2343 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: 6.94 Time building geometry restraints manager: 10.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.44: 7962 1.44 - 1.57: 15039 1.57 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" CB PRO K 111 " pdb=" CG PRO K 111 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.80e+00 bond pdb=" CB PRO C 111 " pdb=" CG PRO C 111 " ideal model delta sigma weight residual 1.492 1.412 0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 1.492 1.412 0.080 5.00e-02 4.00e+02 2.55e+00 bond pdb=" CB PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 1.492 1.413 0.079 5.00e-02 4.00e+02 2.48e+00 bond pdb=" CB PRO E 111 " pdb=" CG PRO E 111 " ideal model delta sigma weight residual 1.492 1.415 0.077 5.00e-02 4.00e+02 2.39e+00 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.25: 617 106.25 - 113.24: 14673 113.24 - 120.22: 11112 120.22 - 127.21: 10025 127.21 - 134.19: 346 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE I 87 " pdb=" CA ILE I 87 " pdb=" C ILE I 87 " ideal model delta sigma weight residual 113.42 107.89 5.53 1.17e+00 7.31e-01 2.23e+01 angle pdb=" N PRO J 165 " pdb=" CA PRO J 165 " pdb=" C PRO J 165 " ideal model delta sigma weight residual 112.47 118.69 -6.22 2.06e+00 2.36e-01 9.12e+00 angle pdb=" N PRO E 165 " pdb=" CA PRO E 165 " pdb=" C PRO E 165 " ideal model delta sigma weight residual 112.47 118.58 -6.11 2.06e+00 2.36e-01 8.80e+00 angle pdb=" CA MET K 163 " pdb=" C MET K 163 " pdb=" O MET K 163 " ideal model delta sigma weight residual 121.78 118.49 3.29 1.12e+00 7.97e-01 8.64e+00 angle pdb=" C GLY B 136 " pdb=" N LEU B 137 " pdb=" CA LEU B 137 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.59e+00 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13582 17.78 - 35.55: 1990 35.55 - 53.33: 437 53.33 - 71.10: 95 71.10 - 88.88: 11 Dihedral angle restraints: 16115 sinusoidal: 6853 harmonic: 9262 Sorted by residual: dihedral pdb=" CA GLU H 170 " pdb=" C GLU H 170 " pdb=" N LEU H 171 " pdb=" CA LEU H 171 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLU C 170 " pdb=" C GLU C 170 " pdb=" N LEU C 171 " pdb=" CA LEU C 171 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU D 164 " pdb=" C LEU D 164 " pdb=" N PRO D 165 " pdb=" CA PRO D 165 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1904 0.038 - 0.076: 1578 0.076 - 0.114: 338 0.114 - 0.152: 63 0.152 - 0.190: 33 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CB VAL F 156 " pdb=" CA VAL F 156 " pdb=" CG1 VAL F 156 " pdb=" CG2 VAL F 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL E 156 " pdb=" CA VAL E 156 " pdb=" CG1 VAL E 156 " pdb=" CG2 VAL E 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CB THR H 132 " pdb=" CA THR H 132 " pdb=" OG1 THR H 132 " pdb=" CG2 THR H 132 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 110 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO J 111 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 110 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO F 111 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 111 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 111 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 145 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO G 146 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 146 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 146 " -0.037 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8950 2.84 - 3.36: 20773 3.36 - 3.87: 39164 3.87 - 4.39: 48457 4.39 - 4.90: 81924 Nonbonded interactions: 199268 Sorted by model distance: nonbonded pdb=" O GLU B 126 " pdb=" OG SER B 130 " model vdw 2.328 2.440 nonbonded pdb=" O GLU E 126 " pdb=" OG SER E 130 " model vdw 2.350 2.440 nonbonded pdb=" O GLU H 126 " pdb=" OG SER H 130 " model vdw 2.351 2.440 nonbonded pdb=" O GLU I 126 " pdb=" OG SER I 130 " model vdw 2.357 2.440 nonbonded pdb=" O GLU A 126 " pdb=" OG SER A 130 " model vdw 2.360 2.440 ... (remaining 199263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 9.670 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 64.690 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 27302 Z= 0.490 Angle : 0.938 10.194 36773 Z= 0.467 Chirality : 0.052 0.190 3916 Planarity : 0.007 0.070 4499 Dihedral : 16.960 88.879 10010 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.14 % Allowed : 5.87 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.00 (0.08), residues: 3146 helix: -4.89 (0.03), residues: 2277 sheet: None (None), residues: 0 loop : -3.00 (0.16), residues: 869 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 570 time to evaluate : 3.205 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 571 average time/residue: 1.6040 time to fit residues: 1041.2020 Evaluate side-chains 410 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 407 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.5549 time to fit residues: 7.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 146 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 102 GLN A 287 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 225 GLN B 287 ASN C 102 GLN C 154 HIS ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 273 GLN C 287 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 287 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 102 GLN E 121 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN G 287 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN H 102 GLN H 121 ASN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN H 287 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 287 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN K 102 GLN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 GLN K 287 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27302 Z= 0.137 Angle : 0.515 12.245 36773 Z= 0.267 Chirality : 0.036 0.131 3916 Planarity : 0.005 0.049 4499 Dihedral : 12.335 59.975 4092 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.72 % Allowed : 14.10 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.11), residues: 3146 helix: -3.42 (0.07), residues: 2266 sheet: None (None), residues: 0 loop : -2.18 (0.19), residues: 880 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 434 time to evaluate : 3.251 Fit side-chains outliers start: 48 outliers final: 15 residues processed: 453 average time/residue: 1.4874 time to fit residues: 778.1470 Evaluate side-chains 346 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 331 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.7728 time to fit residues: 11.1214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 102 GLN B 71 ASN B 102 GLN B 121 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27302 Z= 0.146 Angle : 0.492 11.175 36773 Z= 0.250 Chirality : 0.036 0.136 3916 Planarity : 0.004 0.054 4499 Dihedral : 11.624 59.820 4092 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 15.21 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.14), residues: 3146 helix: -2.14 (0.10), residues: 2200 sheet: None (None), residues: 0 loop : -1.46 (0.20), residues: 946 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 365 time to evaluate : 3.062 Fit side-chains outliers start: 79 outliers final: 37 residues processed: 416 average time/residue: 1.3606 time to fit residues: 657.7926 Evaluate side-chains 370 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 333 time to evaluate : 3.054 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 8 average time/residue: 0.2558 time to fit residues: 7.8672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 297 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 80 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 168 ASN B 71 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 220 GLN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 HIS ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27302 Z= 0.126 Angle : 0.480 14.043 36773 Z= 0.240 Chirality : 0.036 0.136 3916 Planarity : 0.004 0.058 4499 Dihedral : 10.905 59.645 4092 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.33 % Allowed : 15.21 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 3146 helix: -1.45 (0.11), residues: 2200 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 946 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 351 time to evaluate : 2.705 Fit side-chains outliers start: 93 outliers final: 48 residues processed: 412 average time/residue: 1.3082 time to fit residues: 629.6107 Evaluate side-chains 371 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 323 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 31 residues processed: 18 average time/residue: 0.4319 time to fit residues: 16.0599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 152 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 154 HIS ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27302 Z= 0.279 Angle : 0.579 13.482 36773 Z= 0.285 Chirality : 0.041 0.148 3916 Planarity : 0.004 0.046 4499 Dihedral : 11.286 59.930 4092 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 16.32 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 3146 helix: -1.26 (0.11), residues: 2211 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 935 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 348 time to evaluate : 2.983 Fit side-chains outliers start: 100 outliers final: 56 residues processed: 418 average time/residue: 1.3583 time to fit residues: 660.4158 Evaluate side-chains 375 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 319 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 42 residues processed: 17 average time/residue: 0.3117 time to fit residues: 12.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 60.1818 > 50: distance: 67 - 71: 16.606 distance: 71 - 72: 12.766 distance: 72 - 73: 7.249 distance: 72 - 75: 7.950 distance: 73 - 74: 6.239 distance: 73 - 82: 6.110 distance: 75 - 76: 7.627 distance: 76 - 77: 8.262 distance: 82 - 83: 5.380 distance: 82 - 88: 14.749 distance: 83 - 84: 17.310 distance: 83 - 86: 4.630 distance: 84 - 85: 17.445 distance: 84 - 89: 14.948 distance: 86 - 87: 9.034 distance: 87 - 88: 21.045 distance: 89 - 90: 14.087 distance: 90 - 91: 17.320 distance: 90 - 93: 11.016 distance: 91 - 92: 20.747 distance: 91 - 97: 9.883 distance: 93 - 94: 8.289 distance: 94 - 95: 5.536 distance: 94 - 96: 6.068 distance: 97 - 98: 10.759 distance: 97 - 103: 18.262 distance: 98 - 99: 23.141 distance: 98 - 101: 18.681 distance: 99 - 100: 27.661 distance: 99 - 104: 12.959 distance: 101 - 102: 18.739 distance: 102 - 103: 11.836 distance: 104 - 105: 19.281 distance: 105 - 106: 21.978 distance: 105 - 108: 13.718 distance: 106 - 107: 25.377 distance: 106 - 115: 9.830 distance: 108 - 109: 10.245 distance: 109 - 110: 10.552 distance: 109 - 111: 14.778 distance: 110 - 112: 6.765 distance: 111 - 113: 5.545 distance: 112 - 114: 4.619 distance: 113 - 114: 4.940 distance: 115 - 116: 38.250 distance: 115 - 121: 8.299 distance: 116 - 117: 38.412 distance: 116 - 119: 53.294 distance: 117 - 118: 18.299 distance: 117 - 122: 60.182 distance: 119 - 120: 37.335 distance: 120 - 121: 24.166 distance: 122 - 123: 55.735 distance: 123 - 124: 25.208 distance: 123 - 126: 50.490 distance: 124 - 125: 17.730 distance: 124 - 130: 27.842 distance: 126 - 127: 38.781 distance: 127 - 128: 7.873 distance: 128 - 129: 24.373 distance: 130 - 131: 21.712 distance: 130 - 136: 23.105 distance: 131 - 132: 17.441 distance: 131 - 134: 16.179 distance: 132 - 133: 19.747 distance: 132 - 137: 16.852 distance: 134 - 135: 20.775 distance: 135 - 136: 18.048 distance: 137 - 138: 13.124 distance: 138 - 139: 4.851 distance: 138 - 141: 17.331 distance: 139 - 140: 16.175 distance: 139 - 144: 8.920 distance: 141 - 142: 4.192 distance: 141 - 143: 17.476 distance: 144 - 145: 7.179 distance: 145 - 146: 7.842 distance: 145 - 148: 5.460 distance: 146 - 147: 13.518 distance: 146 - 155: 4.958 distance: 147 - 177: 13.036 distance: 148 - 149: 5.364 distance: 149 - 150: 3.873 distance: 150 - 152: 4.771 distance: 152 - 154: 3.608 distance: 153 - 154: 3.439