Starting phenix.real_space_refine on Fri Apr 12 19:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d61_30587/04_2024/7d61_30587_updated.pdb" } resolution = 2.8 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 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 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 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 "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "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 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 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 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "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 "G PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4": "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 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "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 "J PHE 4": "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 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4": "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 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 13.57, per 1000 atoms: 0.51 Number of scatterers: 26664 At special positions: 0 Unit cell: (160.6, 161.7, 107.8, 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=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.44 Conformation dependent library (CDL) restraints added in 4.9 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: 176 helices and 0 sheets defined 64.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.610A pdb=" N THR A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.628A pdb=" N LEU A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.577A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.621A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.581A 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 107 Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.890A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.528A pdb=" N SER A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' 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 175 removed outlier: 3.599A pdb=" N LYS A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 203 removed outlier: 3.536A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.505A pdb=" N PHE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.828A pdb=" N SER A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.516A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 19 through 37 removed outlier: 3.557A pdb=" N THR B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.657A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.678A pdb=" N LEU B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.687A pdb=" N ARG B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 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: 3.828A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' 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 175 removed outlier: 3.548A pdb=" N LYS B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 203 removed outlier: 3.592A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.601A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.808A pdb=" N SER B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.564A pdb=" N VAL B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 37 removed outlier: 3.616A pdb=" N THR C 27 " --> pdb=" O MET C 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 53 through 68 Proline residue: C 58 - end of helix removed outlier: 3.598A pdb=" N LEU C 62 " --> pdb=" O PRO C 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.665A pdb=" N ARG C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 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 106 Processing helix chain 'C' and resid 109 through 119 removed outlier: 3.754A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' 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 167 through 172 removed outlier: 3.539A pdb=" N LYS C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 203 removed outlier: 3.510A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 192 " --> pdb=" O CYS C 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.547A pdb=" N THR C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 239 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.838A pdb=" N SER C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 18 through 37 removed outlier: 3.568A pdb=" N THR D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 53 through 68 Proline residue: D 58 - end of helix removed outlier: 3.608A pdb=" N LEU D 62 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.626A pdb=" N ARG D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 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 107 Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.843A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' 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 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 178 through 203 removed outlier: 3.555A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 192 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.566A pdb=" N PHE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.778A pdb=" N SER D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 18 through 37 removed outlier: 3.595A pdb=" N THR E 27 " --> pdb=" O MET E 23 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 68 removed outlier: 3.529A pdb=" N LEU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.722A pdb=" N LEU E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.678A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 77' Processing helix chain 'E' and resid 95 through 106 removed outlier: 3.521A pdb=" N SER E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.836A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' 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 168 through 175 removed outlier: 3.513A pdb=" N LYS E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 173 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 175' Processing helix chain 'E' and resid 178 through 203 removed outlier: 3.531A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE E 192 " --> pdb=" O CYS E 188 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.537A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.876A pdb=" N SER E 266 " --> pdb=" O TRP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 18 through 37 removed outlier: 3.630A pdb=" N THR F 27 " --> pdb=" O MET F 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 68 removed outlier: 3.611A pdb=" N LEU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.556A pdb=" N LEU F 62 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.584A pdb=" N ARG F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.609A 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 106 Processing helix chain 'F' and resid 109 through 120 removed outlier: 3.749A 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 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' 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 167 through 175 removed outlier: 3.633A pdb=" N LYS F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 203 removed outlier: 3.525A pdb=" N LEU F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.509A pdb=" N PHE F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.848A pdb=" N SER F 266 " --> pdb=" O TRP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.544A pdb=" N VAL F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 19 through 37 removed outlier: 3.654A pdb=" N THR G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 53 through 68 Proline residue: G 58 - end of helix removed outlier: 3.726A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.648A pdb=" N ARG G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 71 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 119 removed outlier: 3.928A 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 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' 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 168 through 175 removed outlier: 3.568A pdb=" N LYS G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 168 through 175' Processing helix chain 'G' and resid 178 through 203 removed outlier: 3.566A pdb=" N LEU G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.579A pdb=" N PHE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 217 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU G 239 " --> pdb=" O ASN G 235 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 243 " --> pdb=" O GLU G 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.672A pdb=" N SER G 266 " --> pdb=" O TRP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'H' and resid 8 through 13 Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.568A pdb=" N THR H 27 " --> pdb=" O MET H 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 68 removed outlier: 3.702A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.642A pdb=" N LEU H 62 " --> pdb=" O PRO H 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.668A pdb=" N ARG H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 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 119 removed outlier: 3.779A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 130 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' 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 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: 3.645A pdb=" N PHE H 192 " --> pdb=" O CYS H 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.524A pdb=" N PHE H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 235 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 239 " --> pdb=" O ASN H 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.856A pdb=" N SER H 266 " --> pdb=" O TRP H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 287 Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 18 through 37 removed outlier: 3.678A pdb=" N THR I 27 " --> pdb=" O MET I 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 68 removed outlier: 3.727A pdb=" N PHE I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.644A pdb=" N LEU I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.695A pdb=" N ARG I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 77' Processing helix chain 'I' and resid 95 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.838A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 130 removed outlier: 3.501A pdb=" N SER I 130 " --> pdb=" O GLU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' 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 167 through 172 removed outlier: 3.518A pdb=" N LYS I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 203 removed outlier: 3.558A pdb=" N LEU I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I 192 " --> pdb=" O CYS I 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 246 removed outlier: 3.601A pdb=" N THR I 217 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS I 221 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU I 224 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN I 235 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I 239 " --> pdb=" O ASN I 235 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS I 243 " --> pdb=" O GLU I 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 266 removed outlier: 3.864A pdb=" N SER I 266 " --> pdb=" O TRP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 287 removed outlier: 3.526A pdb=" N VAL I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 13 Processing helix chain 'J' and resid 18 through 37 removed outlier: 3.634A pdb=" N THR J 27 " --> pdb=" O MET J 23 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.656A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.699A pdb=" N LEU J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.692A pdb=" N ARG J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 71 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 107 Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.889A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 129 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 167 through 172 removed outlier: 3.562A pdb=" N LYS J 172 " --> pdb=" O ASN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 203 removed outlier: 3.554A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE J 192 " --> pdb=" O CYS J 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 246 removed outlier: 3.534A pdb=" N PHE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN J 235 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 239 " --> pdb=" O ASN J 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 266 removed outlier: 3.518A pdb=" N ALA J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER J 266 " --> pdb=" O TRP J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.635A pdb=" N THR K 27 " --> pdb=" O MET K 23 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 35 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.683A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.619A pdb=" N LEU K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.757A pdb=" N ARG K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.635A 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 removed outlier: 3.504A pdb=" N SER K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.841A 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: 3.501A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 192 " --> pdb=" O CYS K 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 246 removed outlier: 3.535A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU K 239 " --> pdb=" O ASN K 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 266 removed outlier: 3.902A pdb=" N SER K 266 " --> pdb=" O TRP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 944 hydrogen bonds defined for protein. 2832 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: 7.33 Time building geometry restraints manager: 11.13 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: 7952 1.44 - 1.56: 15049 1.56 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" C ALA B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.55e+00 bond pdb=" C ALA F 110 " pdb=" N PRO F 111 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.36e-02 5.41e+03 1.49e+00 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CB PRO K 111 " pdb=" CG PRO K 111 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.42e+00 bond pdb=" CB PRO F 111 " pdb=" CG PRO F 111 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.39e+00 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.35: 848 107.35 - 114.04: 15293 114.04 - 120.73: 12042 120.73 - 127.42: 8284 127.42 - 134.10: 306 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE C 7 " pdb=" CA ILE C 7 " pdb=" C ILE C 7 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C GLY E 136 " pdb=" N LEU E 137 " pdb=" CA LEU E 137 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLY G 136 " pdb=" N LEU G 137 " pdb=" CA LEU G 137 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLY F 136 " pdb=" N LEU F 137 " pdb=" CA LEU F 137 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA LEU K 137 " pdb=" CB LEU K 137 " pdb=" CG LEU K 137 " ideal model delta sigma weight residual 116.30 127.00 -10.70 3.50e+00 8.16e-02 9.35e+00 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 13137 15.11 - 30.22: 2132 30.22 - 45.33: 673 45.33 - 60.44: 140 60.44 - 75.55: 33 Dihedral angle restraints: 16115 sinusoidal: 6853 harmonic: 9262 Sorted by residual: dihedral pdb=" CA PRO J 165 " pdb=" C PRO J 165 " pdb=" N THR J 166 " pdb=" CA THR J 166 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO K 165 " pdb=" C PRO K 165 " pdb=" N THR K 166 " pdb=" CA THR K 166 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO D 165 " pdb=" C PRO D 165 " pdb=" N THR D 166 " pdb=" CA THR D 166 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1979 0.029 - 0.057: 1308 0.057 - 0.086: 460 0.086 - 0.114: 139 0.114 - 0.143: 30 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA PRO H 165 " pdb=" N PRO H 165 " pdb=" C PRO H 165 " pdb=" CB PRO H 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO E 165 " pdb=" N PRO E 165 " pdb=" C PRO E 165 " pdb=" CB PRO E 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA PRO K 165 " pdb=" N PRO K 165 " pdb=" C PRO K 165 " pdb=" CB PRO K 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 110 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 111 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 110 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 111 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 110 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO G 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " 0.040 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8998 2.85 - 3.36: 20825 3.36 - 3.88: 39134 3.88 - 4.39: 47983 4.39 - 4.90: 82146 Nonbonded interactions: 199086 Sorted by model distance: nonbonded pdb=" O TRP F 74 " pdb=" OG1 THR F 78 " model vdw 2.340 2.440 nonbonded pdb=" O TRP C 74 " pdb=" OG1 THR C 78 " model vdw 2.358 2.440 nonbonded pdb=" O TRP B 74 " pdb=" OG1 THR B 78 " model vdw 2.369 2.440 nonbonded pdb=" O TRP E 74 " pdb=" OG1 THR E 78 " model vdw 2.369 2.440 nonbonded pdb=" O TRP I 74 " pdb=" OG1 THR I 78 " model vdw 2.373 2.440 ... (remaining 199081 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.030 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 68.480 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.270 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.003 0.060 27302 Z= 0.208 Angle : 0.771 10.702 36773 Z= 0.386 Chirality : 0.042 0.143 3916 Planarity : 0.007 0.072 4499 Dihedral : 16.502 75.548 10010 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -7.13 (0.08), residues: 3146 helix: -4.95 (0.03), residues: 2398 sheet: None (None), residues: 0 loop : -2.69 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 262 HIS 0.006 0.001 HIS D 154 PHE 0.013 0.001 PHE E 68 TYR 0.017 0.002 TYR H 125 ARG 0.007 0.000 ARG E 240 *********************** 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 640 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 3.064 Fit side-chains REVERT: A 88 PHE cc_start: 0.7292 (m-80) cc_final: 0.6979 (m-80) REVERT: A 220 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7777 (tp40) REVERT: A 272 HIS cc_start: 0.7990 (m90) cc_final: 0.7738 (m-70) REVERT: B 88 PHE cc_start: 0.7341 (m-80) cc_final: 0.7105 (m-80) REVERT: B 163 MET cc_start: 0.7893 (ttp) cc_final: 0.7484 (ttm) REVERT: B 176 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 233 TYR cc_start: 0.8864 (m-80) cc_final: 0.8447 (m-80) REVERT: B 273 GLN cc_start: 0.7562 (pt0) cc_final: 0.7225 (pt0) REVERT: C 23 MET cc_start: 0.7937 (ttm) cc_final: 0.7667 (ttp) REVERT: C 31 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 88 PHE cc_start: 0.7495 (m-80) cc_final: 0.6975 (m-80) REVERT: C 243 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7936 (mttt) REVERT: D 31 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 243 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8100 (mttt) REVERT: D 283 ARG cc_start: 0.8352 (ttp80) cc_final: 0.7997 (ttp80) REVERT: E 31 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 32 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7721 (mmm-85) REVERT: E 48 MET cc_start: 0.8101 (tpp) cc_final: 0.7700 (tpt) REVERT: E 176 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7228 (tm-30) REVERT: E 178 GLN cc_start: 0.8769 (mt0) cc_final: 0.8544 (mt0) REVERT: E 273 GLN cc_start: 0.7752 (pt0) cc_final: 0.7519 (pt0) REVERT: F 23 MET cc_start: 0.7937 (ttm) cc_final: 0.7697 (ttp) REVERT: F 31 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 88 PHE cc_start: 0.7290 (m-80) cc_final: 0.6949 (m-80) REVERT: F 163 MET cc_start: 0.7991 (ttp) cc_final: 0.7769 (ttm) REVERT: F 232 ASP cc_start: 0.7822 (t70) cc_final: 0.7618 (t0) REVERT: G 88 PHE cc_start: 0.7097 (m-80) cc_final: 0.6752 (m-80) REVERT: G 176 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7316 (tm-30) REVERT: G 209 TYR cc_start: 0.8075 (t80) cc_final: 0.7852 (t80) REVERT: G 243 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8106 (mttt) REVERT: H 23 MET cc_start: 0.8048 (ttm) cc_final: 0.7818 (ttp) REVERT: H 32 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7626 (mmm-85) REVERT: H 88 PHE cc_start: 0.7120 (m-80) cc_final: 0.6789 (m-80) REVERT: H 176 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7266 (tm-30) REVERT: H 243 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7912 (mttt) REVERT: H 273 GLN cc_start: 0.7473 (pt0) cc_final: 0.7190 (pt0) REVERT: H 283 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8126 (ttp80) REVERT: I 23 MET cc_start: 0.8082 (ttm) cc_final: 0.7802 (ttm) REVERT: I 31 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7316 (tm-30) REVERT: I 88 PHE cc_start: 0.7334 (m-80) cc_final: 0.6817 (m-80) REVERT: I 209 TYR cc_start: 0.7942 (t80) cc_final: 0.7716 (t80) REVERT: I 243 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8006 (mtmm) REVERT: I 273 GLN cc_start: 0.7602 (pt0) cc_final: 0.7395 (pt0) REVERT: J 31 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7595 (tm-30) REVERT: J 88 PHE cc_start: 0.7244 (m-80) cc_final: 0.6829 (m-80) REVERT: J 220 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7728 (tp40) REVERT: J 243 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8032 (mttt) REVERT: J 273 GLN cc_start: 0.7773 (pt0) cc_final: 0.7507 (mt0) REVERT: K 31 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7516 (tm-30) REVERT: K 88 PHE cc_start: 0.7327 (m-80) cc_final: 0.6914 (m-80) REVERT: K 176 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7484 (tm-30) REVERT: K 209 TYR cc_start: 0.8144 (t80) cc_final: 0.7907 (t80) REVERT: K 243 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8077 (mtmm) outliers start: 0 outliers final: 2 residues processed: 640 average time/residue: 1.8903 time to fit residues: 1350.5856 Evaluate side-chains 409 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain D residue 273 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 0.0970 chunk 124 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 168 ASN B 71 ASN B 168 ASN B 228 ASN B 287 ASN C 71 ASN C 168 ASN C 287 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 287 ASN E 14 GLN E 71 ASN E 168 ASN F 47 ASN F 168 ASN F 273 GLN F 287 ASN G 47 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN G 276 GLN G 287 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 168 ASN I 47 ASN I 287 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN K 178 GLN K 225 GLN K 228 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27302 Z= 0.147 Angle : 0.544 14.289 36773 Z= 0.277 Chirality : 0.036 0.147 3916 Planarity : 0.005 0.047 4499 Dihedral : 11.670 73.307 4098 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.40 % Allowed : 12.88 % Favored : 84.72 % 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: -4.56 (0.11), residues: 3146 helix: -3.07 (0.08), residues: 2332 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 60 HIS 0.001 0.000 HIS D 154 PHE 0.011 0.001 PHE C 214 TYR 0.008 0.001 TYR D 278 ARG 0.008 0.000 ARG K 283 *********************** 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 496 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 429 time to evaluate : 3.220 Fit side-chains REVERT: A 176 GLN cc_start: 0.8030 (tt0) cc_final: 0.7432 (tm-30) REVERT: B 22 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: B 23 MET cc_start: 0.7233 (ttm) cc_final: 0.6981 (ttp) REVERT: B 163 MET cc_start: 0.7970 (ttp) cc_final: 0.7638 (ttm) REVERT: B 176 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 273 GLN cc_start: 0.7602 (pt0) cc_final: 0.7271 (pt0) REVERT: C 22 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: C 85 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6770 (tpt170) REVERT: C 243 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7938 (mttt) REVERT: D 25 LEU cc_start: 0.8029 (tt) cc_final: 0.7711 (tp) REVERT: D 85 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6708 (tpt170) REVERT: D 88 PHE cc_start: 0.7004 (m-80) cc_final: 0.6793 (m-80) REVERT: D 129 MET cc_start: 0.8699 (tpt) cc_final: 0.7986 (tpt) REVERT: E 22 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: E 31 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 32 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7536 (mmm-85) REVERT: E 176 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7216 (tm-30) REVERT: E 178 GLN cc_start: 0.8780 (mt0) cc_final: 0.8553 (mt0) REVERT: E 273 GLN cc_start: 0.7811 (pt0) cc_final: 0.7570 (pt0) REVERT: F 23 MET cc_start: 0.7583 (ttm) cc_final: 0.7337 (ttp) REVERT: F 88 PHE cc_start: 0.7127 (m-80) cc_final: 0.6894 (m-80) REVERT: F 163 MET cc_start: 0.7937 (ttp) cc_final: 0.7732 (ttm) REVERT: G 22 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: G 176 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7204 (tm-30) REVERT: G 209 TYR cc_start: 0.7806 (t80) cc_final: 0.7534 (t80) REVERT: G 243 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8024 (mttt) REVERT: H 23 MET cc_start: 0.7915 (ttm) cc_final: 0.7638 (ttm) REVERT: H 25 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7673 (tp) REVERT: H 32 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7568 (mmm-85) REVERT: H 176 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7185 (tm-30) REVERT: H 273 GLN cc_start: 0.7484 (pt0) cc_final: 0.7159 (pt0) REVERT: I 22 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: I 23 MET cc_start: 0.7975 (ttm) cc_final: 0.7755 (ttm) REVERT: I 31 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7329 (tm-30) REVERT: I 243 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7937 (mttt) REVERT: J 220 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7543 (tp40) REVERT: K 176 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7411 (tm-30) REVERT: K 202 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7183 (mmt90) REVERT: K 243 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8051 (mtmm) outliers start: 67 outliers final: 21 residues processed: 462 average time/residue: 1.6663 time to fit residues: 875.4062 Evaluate side-chains 413 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 386 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 280 optimal weight: 20.0000 chunk 302 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 47 ASN B 178 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN F 71 ASN F 273 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN I 168 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27302 Z= 0.182 Angle : 0.543 16.195 36773 Z= 0.269 Chirality : 0.038 0.165 3916 Planarity : 0.004 0.040 4499 Dihedral : 11.158 59.899 4092 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.65 % Allowed : 14.35 % Favored : 82.00 % 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: -2.80 (0.14), residues: 3146 helix: -1.70 (0.10), residues: 2343 sheet: None (None), residues: 0 loop : -1.72 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 60 HIS 0.002 0.000 HIS F 277 PHE 0.017 0.001 PHE J 88 TYR 0.010 0.001 TYR F 278 ARG 0.005 0.000 ARG K 283 *********************** 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 499 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 397 time to evaluate : 3.092 Fit side-chains REVERT: A 85 ARG cc_start: 0.7214 (tpt170) cc_final: 0.7011 (tpt170) REVERT: A 176 GLN cc_start: 0.8052 (tt0) cc_final: 0.7388 (tm-30) REVERT: B 25 LEU cc_start: 0.8045 (tt) cc_final: 0.7824 (tp) REVERT: B 163 MET cc_start: 0.7975 (ttp) cc_final: 0.7689 (ttm) REVERT: B 176 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 273 GLN cc_start: 0.7571 (pt0) cc_final: 0.7254 (pt0) REVERT: C 22 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: C 26 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7622 (mp) REVERT: C 88 PHE cc_start: 0.7356 (m-80) cc_final: 0.7147 (m-80) REVERT: C 243 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7897 (mttt) REVERT: D 88 PHE cc_start: 0.7008 (m-80) cc_final: 0.6764 (m-80) REVERT: D 133 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7775 (mmp80) REVERT: E 25 LEU cc_start: 0.8176 (tt) cc_final: 0.7947 (tp) REVERT: E 32 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7508 (mmm-85) REVERT: E 176 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 273 GLN cc_start: 0.7851 (pt0) cc_final: 0.7616 (pt0) REVERT: G 22 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: G 88 PHE cc_start: 0.7514 (m-80) cc_final: 0.7236 (m-80) REVERT: G 176 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7157 (tm-30) REVERT: G 209 TYR cc_start: 0.7848 (t80) cc_final: 0.7613 (t80) REVERT: H 25 LEU cc_start: 0.8123 (tt) cc_final: 0.7735 (tp) REVERT: H 32 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7673 (mmm-85) REVERT: H 176 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7105 (tm-30) REVERT: H 250 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7364 (mmp80) REVERT: H 273 GLN cc_start: 0.7501 (pt0) cc_final: 0.7224 (pt0) REVERT: I 22 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: I 23 MET cc_start: 0.7864 (ttm) cc_final: 0.7607 (ttm) REVERT: I 31 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7406 (tm-30) REVERT: I 243 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7926 (mttt) REVERT: J 133 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7764 (mmp80) REVERT: J 220 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7616 (tp40) REVERT: K 11 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: K 176 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7265 (tm-30) REVERT: K 202 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7271 (mmt90) REVERT: K 231 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8661 (tp) REVERT: K 235 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8170 (m110) REVERT: K 243 LYS cc_start: 0.8249 (mtmt) cc_final: 0.8008 (mttt) outliers start: 102 outliers final: 56 residues processed: 466 average time/residue: 1.6333 time to fit residues: 864.1226 Evaluate side-chains 445 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 382 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 3.9990 chunk 210 optimal weight: 0.0050 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 overall best weight: 1.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 178 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN H 47 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27302 Z= 0.206 Angle : 0.544 15.432 36773 Z= 0.267 Chirality : 0.039 0.162 3916 Planarity : 0.004 0.035 4499 Dihedral : 10.998 59.971 4092 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.12 % Allowed : 15.43 % Favored : 80.46 % 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: -2.00 (0.15), residues: 3146 helix: -1.13 (0.11), residues: 2354 sheet: None (None), residues: 0 loop : -1.37 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 262 HIS 0.002 0.000 HIS B 154 PHE 0.013 0.001 PHE H 88 TYR 0.010 0.001 TYR D 278 ARG 0.005 0.000 ARG F 95 *********************** 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 512 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 397 time to evaluate : 3.204 Fit side-chains REVERT: A 85 ARG cc_start: 0.7314 (tpt170) cc_final: 0.7097 (tpt170) REVERT: A 88 PHE cc_start: 0.7461 (m-80) cc_final: 0.7100 (m-80) REVERT: A 176 GLN cc_start: 0.8070 (tt0) cc_final: 0.7468 (tm-30) REVERT: B 25 LEU cc_start: 0.8084 (tt) cc_final: 0.7799 (tp) REVERT: B 133 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.7834 (mmp80) REVERT: B 163 MET cc_start: 0.7959 (ttp) cc_final: 0.7713 (ttm) REVERT: B 176 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7207 (tm-30) REVERT: B 273 GLN cc_start: 0.7613 (pt0) cc_final: 0.7324 (pt0) REVERT: C 26 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7591 (mp) REVERT: C 85 ARG cc_start: 0.6914 (tpt170) cc_final: 0.6682 (tpt170) REVERT: C 88 PHE cc_start: 0.7287 (m-80) cc_final: 0.7070 (m-80) REVERT: C 243 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7898 (mttt) REVERT: D 32 ARG cc_start: 0.7905 (tpm-80) cc_final: 0.7669 (tpm-80) REVERT: D 133 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7865 (mmp80) REVERT: D 204 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7844 (mtm180) REVERT: E 25 LEU cc_start: 0.8143 (tt) cc_final: 0.7932 (tp) REVERT: E 32 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7453 (mmm-85) REVERT: E 176 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7251 (tm-30) REVERT: E 273 GLN cc_start: 0.7775 (pt0) cc_final: 0.7513 (pt0) REVERT: F 31 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7668 (tm-30) REVERT: F 44 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (p) REVERT: G 22 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: G 176 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7196 (tm-30) REVERT: H 25 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7652 (tp) REVERT: H 32 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7658 (mmm-85) REVERT: H 44 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8310 (p) REVERT: H 133 ARG cc_start: 0.8176 (tpp-160) cc_final: 0.7865 (mmp80) REVERT: H 176 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7099 (tm-30) REVERT: H 273 GLN cc_start: 0.7487 (pt0) cc_final: 0.7233 (pt0) REVERT: I 22 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: I 23 MET cc_start: 0.7717 (ttm) cc_final: 0.7465 (ttm) REVERT: I 31 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7438 (tm-30) REVERT: I 243 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7881 (mttt) REVERT: J 133 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7756 (mmp80) REVERT: J 140 LEU cc_start: 0.8525 (mt) cc_final: 0.8294 (mt) REVERT: J 220 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7640 (tp40) REVERT: K 11 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: K 176 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7291 (tm-30) REVERT: K 202 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7291 (mmt180) REVERT: K 231 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8648 (tp) REVERT: K 235 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8107 (m110) REVERT: K 243 LYS cc_start: 0.8266 (mtmt) cc_final: 0.8013 (mtmm) outliers start: 115 outliers final: 67 residues processed: 471 average time/residue: 1.6618 time to fit residues: 886.2515 Evaluate side-chains 459 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 382 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 273 GLN Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 267 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27302 Z= 0.231 Angle : 0.556 15.333 36773 Z= 0.274 Chirality : 0.040 0.162 3916 Planarity : 0.004 0.032 4499 Dihedral : 10.976 58.431 4092 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.44 % Allowed : 16.57 % Favored : 79.99 % 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: -1.57 (0.15), residues: 3146 helix: -0.82 (0.11), residues: 2354 sheet: None (None), residues: 0 loop : -1.19 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 262 HIS 0.002 0.000 HIS D 154 PHE 0.022 0.001 PHE F 88 TYR 0.010 0.001 TYR F 278 ARG 0.006 0.000 ARG A 95 *********************** 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 480 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 384 time to evaluate : 3.201 Fit side-chains REVERT: A 32 ARG cc_start: 0.8012 (tpm-80) cc_final: 0.7760 (tpm-80) REVERT: A 88 PHE cc_start: 0.7544 (m-80) cc_final: 0.7245 (m-80) REVERT: A 176 GLN cc_start: 0.8086 (tt0) cc_final: 0.7479 (tm-30) REVERT: B 25 LEU cc_start: 0.8101 (tt) cc_final: 0.7831 (tp) REVERT: B 133 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7777 (mmp80) REVERT: B 163 MET cc_start: 0.7960 (ttp) cc_final: 0.7724 (ttm) REVERT: B 176 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 243 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7905 (mttt) REVERT: D 133 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7890 (mmp80) REVERT: E 11 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: E 25 LEU cc_start: 0.8030 (tt) cc_final: 0.7812 (tp) REVERT: E 147 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7790 (tptt) REVERT: E 176 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7283 (tm-30) REVERT: E 273 GLN cc_start: 0.7782 (pt0) cc_final: 0.7529 (pt0) REVERT: F 88 PHE cc_start: 0.7502 (m-80) cc_final: 0.7277 (m-80) REVERT: G 176 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7240 (tm-30) REVERT: H 25 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7719 (tp) REVERT: H 32 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7615 (mmm-85) REVERT: H 133 ARG cc_start: 0.8187 (tpp-160) cc_final: 0.7865 (mmp80) REVERT: H 176 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7219 (tm-30) REVERT: H 250 ARG cc_start: 0.7699 (mpt180) cc_final: 0.7325 (mmp80) REVERT: H 273 GLN cc_start: 0.7445 (pt0) cc_final: 0.7191 (pt0) REVERT: I 22 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: I 31 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7483 (tm-30) REVERT: I 243 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7888 (mttt) REVERT: J 25 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7674 (tt) REVERT: J 140 LEU cc_start: 0.8535 (mt) cc_final: 0.8300 (mt) REVERT: J 220 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7635 (tp40) REVERT: K 11 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: K 25 LEU cc_start: 0.8050 (tt) cc_final: 0.7837 (tp) REVERT: K 176 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7276 (tm-30) REVERT: K 235 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8069 (m110) REVERT: K 243 LYS cc_start: 0.8280 (mtmt) cc_final: 0.8019 (mtmm) outliers start: 96 outliers final: 67 residues processed: 442 average time/residue: 1.5972 time to fit residues: 804.4196 Evaluate side-chains 468 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 395 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 273 GLN Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27302 Z= 0.226 Angle : 0.549 15.829 36773 Z= 0.271 Chirality : 0.039 0.164 3916 Planarity : 0.004 0.032 4499 Dihedral : 10.925 59.593 4092 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.40 % Allowed : 17.32 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3146 helix: -0.56 (0.11), residues: 2310 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 262 HIS 0.002 0.000 HIS D 154 PHE 0.019 0.001 PHE F 88 TYR 0.010 0.001 TYR E 278 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 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 484 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 389 time to evaluate : 3.111 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8001 (tpm-80) cc_final: 0.7623 (tpm-80) REVERT: A 176 GLN cc_start: 0.8081 (tt0) cc_final: 0.7472 (tm-30) REVERT: B 25 LEU cc_start: 0.8083 (tt) cc_final: 0.7781 (tp) REVERT: B 133 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7746 (mmp80) REVERT: B 163 MET cc_start: 0.7967 (ttp) cc_final: 0.7738 (ttm) REVERT: B 176 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7263 (tm-30) REVERT: C 243 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7881 (mttt) REVERT: D 133 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7841 (mmp80) REVERT: E 11 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: E 176 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7222 (tm-30) REVERT: E 273 GLN cc_start: 0.7759 (pt0) cc_final: 0.7541 (pt0) REVERT: F 65 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8149 (tp) REVERT: G 32 ARG cc_start: 0.7916 (tpm-80) cc_final: 0.7693 (tpm-80) REVERT: G 176 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7197 (tm-30) REVERT: H 25 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (tp) REVERT: H 32 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7701 (mmm-85) REVERT: H 44 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (p) REVERT: H 48 MET cc_start: 0.7836 (tpp) cc_final: 0.7625 (tpt) REVERT: H 133 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7856 (mmp80) REVERT: H 176 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7209 (tm-30) REVERT: H 273 GLN cc_start: 0.7436 (pt0) cc_final: 0.7192 (pt0) REVERT: I 31 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7491 (tm-30) REVERT: I 147 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7617 (tppt) REVERT: I 243 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7868 (mttt) REVERT: J 25 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7698 (tt) REVERT: J 140 LEU cc_start: 0.8554 (mt) cc_final: 0.8340 (mt) REVERT: J 220 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7620 (tp40) REVERT: K 11 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6550 (m-10) REVERT: K 25 LEU cc_start: 0.8035 (tt) cc_final: 0.7828 (tp) REVERT: K 176 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7296 (tm-30) REVERT: K 235 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8036 (m110) REVERT: K 243 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7996 (mtmm) outliers start: 95 outliers final: 67 residues processed: 450 average time/residue: 1.6482 time to fit residues: 842.1402 Evaluate side-chains 457 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 383 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27302 Z= 0.222 Angle : 0.545 14.911 36773 Z= 0.270 Chirality : 0.039 0.156 3916 Planarity : 0.004 0.032 4499 Dihedral : 10.835 59.078 4092 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.40 % Allowed : 17.82 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3146 helix: -0.38 (0.11), residues: 2310 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 262 HIS 0.002 0.000 HIS B 154 PHE 0.023 0.001 PHE J 88 TYR 0.010 0.001 TYR F 278 ARG 0.006 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 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 481 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 386 time to evaluate : 3.202 Fit side-chains REVERT: A 176 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: B 25 LEU cc_start: 0.8190 (tt) cc_final: 0.7836 (tp) REVERT: B 163 MET cc_start: 0.7986 (ttp) cc_final: 0.7760 (ttm) REVERT: B 176 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 243 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7873 (mttt) REVERT: D 85 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6952 (tpt170) REVERT: D 133 ARG cc_start: 0.8115 (tpp-160) cc_final: 0.7797 (mmp80) REVERT: D 283 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7764 (ttp80) REVERT: E 11 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6619 (m-10) REVERT: E 176 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7197 (tm-30) REVERT: E 273 GLN cc_start: 0.7739 (pt0) cc_final: 0.7519 (pt0) REVERT: G 14 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7388 (mm-40) REVERT: G 176 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7196 (tm-30) REVERT: H 25 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7705 (tp) REVERT: H 32 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7666 (mmm-85) REVERT: H 48 MET cc_start: 0.7834 (tpp) cc_final: 0.7623 (tpt) REVERT: H 133 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7830 (mmp80) REVERT: H 176 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7217 (tm-30) REVERT: H 273 GLN cc_start: 0.7428 (pt0) cc_final: 0.7207 (pt0) REVERT: I 31 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7516 (tm-30) REVERT: I 147 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7645 (tppt) REVERT: I 243 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7864 (mttt) REVERT: J 25 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (tp) REVERT: J 140 LEU cc_start: 0.8553 (mt) cc_final: 0.8341 (mt) REVERT: J 148 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: J 220 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7621 (tp40) REVERT: K 11 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6591 (m-10) REVERT: K 176 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7289 (tm-30) REVERT: K 235 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8045 (m110) REVERT: K 243 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7991 (mtmm) outliers start: 95 outliers final: 67 residues processed: 448 average time/residue: 1.6872 time to fit residues: 854.9634 Evaluate side-chains 457 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 383 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 189 SER Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN J 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN K 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27302 Z= 0.136 Angle : 0.491 14.390 36773 Z= 0.244 Chirality : 0.036 0.155 3916 Planarity : 0.003 0.032 4499 Dihedral : 10.306 58.895 4092 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.40 % Allowed : 19.18 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 3146 helix: 0.17 (0.12), residues: 2244 sheet: None (None), residues: 0 loop : -1.24 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.002 0.000 HIS H 154 PHE 0.027 0.001 PHE F 88 TYR 0.010 0.001 TYR J 278 ARG 0.006 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 8 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 460 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 393 time to evaluate : 3.148 Fit side-chains REVERT: A 176 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: B 22 PHE cc_start: 0.7649 (t80) cc_final: 0.7321 (t80) REVERT: B 25 LEU cc_start: 0.8178 (tt) cc_final: 0.7851 (tp) REVERT: B 163 MET cc_start: 0.8003 (ttp) cc_final: 0.7780 (ttm) REVERT: B 176 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7160 (tm-30) REVERT: D 133 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7823 (mmp80) REVERT: D 176 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7315 (tm-30) REVERT: E 11 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: E 176 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7210 (tm-30) REVERT: G 176 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7229 (tm-30) REVERT: H 25 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7571 (tp) REVERT: H 88 PHE cc_start: 0.7100 (m-80) cc_final: 0.6776 (m-80) REVERT: H 133 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7880 (mmp80) REVERT: H 176 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7360 (tm-30) REVERT: I 147 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7648 (tppt) REVERT: J 113 MET cc_start: 0.7588 (mtp) cc_final: 0.7358 (ttp) REVERT: J 220 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7588 (tp40) REVERT: K 11 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: K 176 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7339 (tm-30) REVERT: K 235 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7974 (m110) REVERT: K 243 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7963 (mtmm) outliers start: 67 outliers final: 37 residues processed: 426 average time/residue: 1.6900 time to fit residues: 814.1044 Evaluate side-chains 429 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 387 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 0.0870 chunk 259 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 ASN J 273 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27302 Z= 0.189 Angle : 0.524 13.389 36773 Z= 0.261 Chirality : 0.038 0.147 3916 Planarity : 0.003 0.031 4499 Dihedral : 10.369 59.953 4092 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.29 % Allowed : 20.11 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 3146 helix: 0.24 (0.12), residues: 2244 sheet: None (None), residues: 0 loop : -1.19 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 60 HIS 0.002 0.000 HIS D 154 PHE 0.026 0.001 PHE F 88 TYR 0.009 0.001 TYR F 278 ARG 0.007 0.000 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 9 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 455 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 391 time to evaluate : 3.017 Fit side-chains REVERT: A 176 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 22 PHE cc_start: 0.7568 (t80) cc_final: 0.7212 (t80) REVERT: B 25 LEU cc_start: 0.8185 (tt) cc_final: 0.7672 (mm) REVERT: B 163 MET cc_start: 0.8013 (ttp) cc_final: 0.7807 (ttm) REVERT: B 176 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7237 (tm-30) REVERT: D 85 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6902 (tpt170) REVERT: D 176 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7292 (tm-30) REVERT: E 11 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6610 (m-10) REVERT: E 85 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6425 (tpt170) REVERT: E 88 PHE cc_start: 0.7135 (m-80) cc_final: 0.6751 (m-80) REVERT: E 176 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7233 (tm-30) REVERT: G 14 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7424 (mm-40) REVERT: G 176 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7254 (tm-30) REVERT: H 25 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7560 (tp) REVERT: H 44 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (p) REVERT: H 133 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.7883 (mmp80) REVERT: H 176 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7345 (tm-30) REVERT: J 129 MET cc_start: 0.8761 (tpp) cc_final: 0.8561 (tpt) REVERT: J 147 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7927 (tptt) REVERT: J 220 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7563 (tp40) REVERT: K 11 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: K 176 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7290 (tm-30) REVERT: K 235 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8011 (m110) REVERT: K 243 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7955 (mtmm) outliers start: 64 outliers final: 43 residues processed: 420 average time/residue: 1.7307 time to fit residues: 820.2168 Evaluate side-chains 448 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 399 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.0980 chunk 292 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27302 Z= 0.182 Angle : 0.524 13.324 36773 Z= 0.261 Chirality : 0.038 0.148 3916 Planarity : 0.003 0.032 4499 Dihedral : 10.319 59.717 4092 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.90 % Allowed : 20.69 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 3146 helix: 0.33 (0.12), residues: 2244 sheet: None (None), residues: 0 loop : -1.16 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 262 HIS 0.002 0.000 HIS D 154 PHE 0.026 0.001 PHE F 88 TYR 0.010 0.001 TYR H 209 ARG 0.007 0.000 ARG H 283 ********************** REFINEMENT MACRO_CYCLE 10 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 442 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 389 time to evaluate : 3.172 Fit side-chains REVERT: A 176 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: B 22 PHE cc_start: 0.7548 (t80) cc_final: 0.7199 (t80) REVERT: B 25 LEU cc_start: 0.8151 (tt) cc_final: 0.7650 (mm) REVERT: B 163 MET cc_start: 0.7889 (ttp) cc_final: 0.7618 (ttm) REVERT: B 176 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7244 (tm-30) REVERT: D 85 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6924 (tpt170) REVERT: D 176 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7299 (tm-30) REVERT: E 11 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6631 (m-10) REVERT: E 85 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6443 (tpt170) REVERT: E 88 PHE cc_start: 0.7162 (m-80) cc_final: 0.6771 (m-80) REVERT: E 176 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7211 (tm-30) REVERT: G 176 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7250 (tm-30) REVERT: H 25 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7562 (tp) REVERT: H 133 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7860 (mmp80) REVERT: H 176 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7347 (tm-30) REVERT: J 113 MET cc_start: 0.7803 (mtp) cc_final: 0.7530 (ttm) REVERT: J 147 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7910 (tptt) REVERT: J 220 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7557 (tp40) REVERT: K 11 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6618 (m-10) REVERT: K 176 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7289 (tm-30) REVERT: K 235 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8006 (m110) REVERT: K 243 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7936 (mttt) outliers start: 53 outliers final: 41 residues processed: 412 average time/residue: 1.7684 time to fit residues: 820.0264 Evaluate side-chains 436 residues out of total 2816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 390 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 235 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107649 restraints weight = 29153.873| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.08 r_work: 0.3049 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27302 Z= 0.164 Angle : 0.514 13.154 36773 Z= 0.256 Chirality : 0.037 0.148 3916 Planarity : 0.003 0.045 4499 Dihedral : 10.132 59.927 4092 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.00 % Allowed : 20.65 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 3146 helix: 0.45 (0.12), residues: 2255 sheet: None (None), residues: 0 loop : -1.07 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 60 HIS 0.002 0.000 HIS H 154 PHE 0.028 0.001 PHE K 88 TYR 0.009 0.001 TYR H 209 ARG 0.009 0.000 ARG H 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12439.11 seconds wall clock time: 222 minutes 34.11 seconds (13354.11 seconds total)