Starting phenix.real_space_refine on Sun Jul 5 07:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.map" model { file = "/net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d65_30589/07_2026/7d65_30589.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 101 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 5.72, per 1000 atoms: 0.21 Number of scatterers: 26664 At special positions: 0 Unit cell: (158.4, 157.3, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 P 55 15.00 O 4862 8.00 N 4224 7.00 C 17303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 127 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 127 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 149 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 158 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 127 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 158 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 127 " distance=2.04 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 158 " distance=2.03 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 149 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 127 " distance=2.04 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 149 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 127 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 142 " - pdb=" SG CYS K 149 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 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... Secondary structure from input PDB file: 190 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.852A pdb=" N PHE A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.508A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 69 removed outlier: 3.673A pdb=" N LEU A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.604A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.737A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.590A pdb=" N LYS A 86 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.509A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.643A pdb=" N GLU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.692A pdb=" N LYS A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 177 through 204 removed outlier: 3.523A pdb=" N ILE A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.585A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.737A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.555A pdb=" N ALA A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.588A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.902A pdb=" N PHE B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 38 removed outlier: 3.548A pdb=" N GLY B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 69 removed outlier: 3.798A pdb=" N LEU B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Proline residue: B 58 - end of helix removed outlier: 3.513A pdb=" N LEU B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.681A pdb=" N ARG B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.595A pdb=" N LYS B 86 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.616A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.642A pdb=" N GLU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.508A pdb=" N TRP B 150 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.730A pdb=" N LYS B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.533A pdb=" N LEU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.590A pdb=" N TRP B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.525A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.586A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 231 through 247 removed outlier: 3.702A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.563A pdb=" N ALA B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.675A pdb=" N VAL B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 9 through 14 removed outlier: 3.815A pdb=" N GLN C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 38 removed outlier: 3.558A pdb=" N GLY C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.629A pdb=" N LEU C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.803A pdb=" N PHE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Proline residue: C 58 - end of helix removed outlier: 3.504A pdb=" N LEU C 62 " --> pdb=" O PRO C 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.644A pdb=" N ARG C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.541A pdb=" N LYS C 86 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 108 Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.614A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.758A pdb=" N GLU C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY C 131 " --> pdb=" O CYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.710A pdb=" N LYS C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 204 removed outlier: 3.689A pdb=" N SER C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP C 184 " --> pdb=" O GLN C 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.532A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.850A pdb=" N ARG C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 removed outlier: 3.595A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.601A pdb=" N VAL C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 9 Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.692A pdb=" N GLN D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.519A pdb=" N GLY D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 69 removed outlier: 3.527A pdb=" N LEU D 52 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Proline residue: D 58 - end of helix removed outlier: 3.545A pdb=" N LEU D 62 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 removed outlier: 3.780A pdb=" N ARG D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.582A pdb=" N LYS D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.525A pdb=" N TYR D 98 " --> pdb=" O CYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.627A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 131 removed outlier: 3.664A pdb=" N GLU D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY D 131 " --> pdb=" O CYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.696A pdb=" N LYS D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.582A pdb=" N LEU D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 204 removed outlier: 3.540A pdb=" N ILE D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 192 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 204 " --> pdb=" O TYR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.658A pdb=" N THR D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 234 through 247 removed outlier: 3.838A pdb=" N ARG D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 removed outlier: 3.637A pdb=" N ALA D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 287 removed outlier: 3.523A pdb=" N VAL D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.772A pdb=" N GLN E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 38 removed outlier: 3.552A pdb=" N GLY E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 69 removed outlier: 3.630A pdb=" N LEU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Proline residue: E 58 - end of helix removed outlier: 3.529A pdb=" N LEU E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.743A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.558A pdb=" N LYS E 86 " --> pdb=" O ASN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.618A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 131 removed outlier: 3.659A pdb=" N GLU E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY E 131 " --> pdb=" O CYS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.621A pdb=" N TRP E 150 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.738A pdb=" N LYS E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 204 removed outlier: 3.505A pdb=" N LEU E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP E 184 " --> pdb=" O GLN E 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 192 " --> pdb=" O CYS E 188 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 204 " --> pdb=" O TYR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 230 removed outlier: 3.542A pdb=" N PHE E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 247 removed outlier: 3.926A pdb=" N ARG E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 265 removed outlier: 3.605A pdb=" N ALA E 264 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 removed outlier: 3.674A pdb=" N VAL E 284 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 9 Processing helix chain 'F' and resid 9 through 14 removed outlier: 3.641A pdb=" N GLN F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 38 removed outlier: 3.501A pdb=" N GLY F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 69 removed outlier: 3.629A pdb=" N LEU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Proline residue: F 58 - end of helix removed outlier: 3.518A pdb=" N LEU F 62 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 removed outlier: 4.139A pdb=" N TRP F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.589A pdb=" N LYS F 86 " --> pdb=" O ASN F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 Processing helix chain 'F' and resid 108 through 121 removed outlier: 3.741A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 131 removed outlier: 4.104A pdb=" N GLY F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.734A pdb=" N LYS F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.626A pdb=" N LEU F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 171 through 176' Processing helix chain 'F' and resid 178 through 204 removed outlier: 3.686A pdb=" N TRP F 184 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 189 " --> pdb=" O CYS F 185 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG F 204 " --> pdb=" O TYR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 225 removed outlier: 3.569A pdb=" N THR F 217 " --> pdb=" O SER F 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 247 removed outlier: 3.813A pdb=" N ASN F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG F 240 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 265 removed outlier: 3.664A pdb=" N ALA F 264 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 287 removed outlier: 3.536A pdb=" N VAL F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 Processing helix chain 'G' and resid 9 through 14 removed outlier: 3.654A pdb=" N GLN G 14 " --> pdb=" O PHE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 38 removed outlier: 3.750A pdb=" N GLY G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 69 removed outlier: 3.723A pdb=" N LEU G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Proline residue: G 58 - end of helix removed outlier: 3.564A pdb=" N LEU G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 78 removed outlier: 3.673A pdb=" N ARG G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.557A pdb=" N LYS G 86 " --> pdb=" O ASN G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 108 removed outlier: 3.513A pdb=" N TYR G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 removed outlier: 3.530A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 131 removed outlier: 3.997A pdb=" N GLY G 131 " --> pdb=" O CYS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.510A pdb=" N TRP G 150 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.684A pdb=" N LYS G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 177 through 204 removed outlier: 3.626A pdb=" N TRP G 184 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 204 " --> pdb=" O TYR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 230 removed outlier: 3.590A pdb=" N GLN G 220 " --> pdb=" O LYS G 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU G 224 " --> pdb=" O GLN G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 247 removed outlier: 3.981A pdb=" N ARG G 240 " --> pdb=" O LYS G 236 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 265 removed outlier: 3.590A pdb=" N ALA G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 287 removed outlier: 3.568A pdb=" N VAL G 284 " --> pdb=" O THR G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 9 Processing helix chain 'H' and resid 9 through 14 removed outlier: 3.729A pdb=" N GLN H 14 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 38 removed outlier: 3.528A pdb=" N GLY H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 69 removed outlier: 3.565A pdb=" N LEU H 52 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Proline residue: H 58 - end of helix removed outlier: 3.561A pdb=" N LEU H 62 " --> pdb=" O PRO H 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.744A pdb=" N ARG H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.594A pdb=" N LYS H 86 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 108 Processing helix chain 'H' and resid 108 through 121 removed outlier: 3.575A pdb=" N VAL H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 131 removed outlier: 3.766A pdb=" N GLU H 126 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY H 131 " --> pdb=" O CYS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.706A pdb=" N LYS H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 204 removed outlier: 3.508A pdb=" N LEU H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP H 184 " --> pdb=" O GLN H 180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 187 " --> pdb=" O GLY H 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 230 removed outlier: 3.601A pdb=" N THR H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS H 223 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU H 224 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 247 removed outlier: 3.975A pdb=" N ARG H 240 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS H 243 " --> pdb=" O GLU H 239 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 removed outlier: 3.613A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 287 removed outlier: 3.648A pdb=" N VAL H 284 " --> pdb=" O THR H 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 14 removed outlier: 3.891A pdb=" N PHE I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 14 " --> pdb=" O PHE I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 38 removed outlier: 3.552A pdb=" N GLY I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 removed outlier: 3.702A pdb=" N LEU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 69 removed outlier: 3.628A pdb=" N PHE I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Proline residue: I 58 - end of helix removed outlier: 3.520A pdb=" N LEU I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 78 removed outlier: 3.691A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.591A pdb=" N LYS I 86 " --> pdb=" O ASN I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 107 removed outlier: 3.512A pdb=" N TYR I 98 " --> pdb=" O CYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 3.720A pdb=" N VAL I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL I 117 " --> pdb=" O MET I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 131 removed outlier: 3.557A pdb=" N GLU I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY I 131 " --> pdb=" O CYS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.628A pdb=" N TRP I 150 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.765A pdb=" N LYS I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.610A pdb=" N LEU I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 171 through 176' Processing helix chain 'I' and resid 177 through 204 removed outlier: 3.505A pdb=" N ILE I 181 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP I 184 " --> pdb=" O GLN I 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER I 189 " --> pdb=" O CYS I 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE I 192 " --> pdb=" O CYS I 188 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG I 204 " --> pdb=" O TYR I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 221 removed outlier: 3.542A pdb=" N THR I 217 " --> pdb=" O SER I 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 220 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 230 removed outlier: 3.508A pdb=" N PHE I 230 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 247 removed outlier: 4.053A pdb=" N ARG I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 265 removed outlier: 3.608A pdb=" N ALA I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 265 " --> pdb=" O ALA I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 287 removed outlier: 3.551A pdb=" N VAL I 284 " --> pdb=" O THR I 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I 285 " --> pdb=" O LEU I 281 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 286 " --> pdb=" O HIS I 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 14 removed outlier: 3.716A pdb=" N GLN J 14 " --> pdb=" O PHE J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 38 removed outlier: 3.548A pdb=" N GLY J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 69 removed outlier: 3.832A pdb=" N LEU J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Proline residue: J 58 - end of helix removed outlier: 3.530A pdb=" N LEU J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 78 removed outlier: 3.741A pdb=" N ARG J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.559A pdb=" N LYS J 86 " --> pdb=" O ASN J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 107 Processing helix chain 'J' and resid 108 through 121 removed outlier: 3.583A pdb=" N VAL J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 131 removed outlier: 3.985A pdb=" N GLY J 131 " --> pdb=" O CYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.733A pdb=" N LYS J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 removed outlier: 3.604A pdb=" N LEU J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 191 removed outlier: 3.551A pdb=" N LEU J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP J 184 " --> pdb=" O GLN J 180 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE J 187 " --> pdb=" O GLY J 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER J 189 " --> pdb=" O CYS J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 204 removed outlier: 3.603A pdb=" N THR J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 204 " --> pdb=" O TYR J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 225 removed outlier: 3.590A pdb=" N PHE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR J 217 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN J 220 " --> pdb=" O LYS J 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 230 Processing helix chain 'J' and resid 234 through 247 removed outlier: 3.942A pdb=" N ARG J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 265 removed outlier: 3.575A pdb=" N ALA J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 287 removed outlier: 3.507A pdb=" N VAL J 284 " --> pdb=" O THR J 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL J 285 " --> pdb=" O LEU J 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 14 removed outlier: 3.893A pdb=" N PHE K 10 " --> pdb=" O GLY K 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN K 14 " --> pdb=" O PHE K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 38 removed outlier: 3.552A pdb=" N GLY K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 69 removed outlier: 3.756A pdb=" N LEU K 52 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Proline residue: K 58 - end of helix removed outlier: 3.526A pdb=" N LEU K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 removed outlier: 3.736A pdb=" N ARG K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE K 77 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.533A pdb=" N LYS K 86 " --> pdb=" O ASN K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 108 Processing helix chain 'K' and resid 108 through 121 removed outlier: 3.871A pdb=" N VAL K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 131 removed outlier: 4.010A pdb=" N GLY K 131 " --> pdb=" O CYS K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 152 through 156 removed outlier: 3.702A pdb=" N LYS K 155 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 176 removed outlier: 3.647A pdb=" N LEU K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 204 removed outlier: 3.555A pdb=" N ILE K 181 " --> pdb=" O ALA K 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER K 189 " --> pdb=" O CYS K 185 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE K 192 " --> pdb=" O CYS K 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER K 194 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG K 204 " --> pdb=" O TYR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 230 removed outlier: 3.598A pdb=" N THR K 217 " --> pdb=" O SER K 213 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS K 223 " --> pdb=" O ALA K 219 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 247 removed outlier: 3.840A pdb=" N ASN K 235 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 237 " --> pdb=" O TYR K 233 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG K 240 " --> pdb=" O LYS K 236 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 265 removed outlier: 3.555A pdb=" N ALA K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 265 " --> pdb=" O ALA K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 287 removed outlier: 3.576A pdb=" N VAL K 284 " --> pdb=" O THR K 280 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3159 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: 4.24 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3960 1.31 - 1.44: 7962 1.44 - 1.57: 15039 1.57 - 1.69: 55 1.69 - 1.82: 286 Bond restraints: 27302 Sorted by residual: bond pdb=" C12 PA8 B 305 " pdb=" O7 PA8 B 305 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C12 PA8 A 305 " pdb=" O7 PA8 A 305 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C12 PA8 I 305 " pdb=" O7 PA8 I 305 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C12 PA8 F 305 " pdb=" O7 PA8 F 305 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C12 PA8 C 305 " pdb=" O7 PA8 C 305 " ideal model delta sigma weight residual 1.327 1.409 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 27297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 34731 2.20 - 4.41: 1280 4.41 - 6.61: 521 6.61 - 8.82: 124 8.82 - 11.02: 117 Bond angle restraints: 36773 Sorted by residual: angle pdb=" N ILE I 87 " pdb=" CA ILE I 87 " pdb=" C ILE I 87 " ideal model delta sigma weight residual 113.42 107.89 5.53 1.17e+00 7.31e-01 2.23e+01 angle pdb=" C13 PA8 J 305 " pdb=" C12 PA8 J 305 " pdb=" O7 PA8 J 305 " ideal model delta sigma weight residual 111.38 122.40 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C13 PA8 B 305 " pdb=" C12 PA8 B 305 " pdb=" O7 PA8 B 305 " ideal model delta sigma weight residual 111.38 122.31 -10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C13 PA8 D 305 " pdb=" C12 PA8 D 305 " pdb=" O7 PA8 D 305 " ideal model delta sigma weight residual 111.38 122.28 -10.90 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C13 PA8 C 305 " pdb=" C12 PA8 C 305 " pdb=" O7 PA8 C 305 " ideal model delta sigma weight residual 111.38 122.17 -10.79 3.00e+00 1.11e-01 1.29e+01 ... (remaining 36768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13544 17.78 - 35.55: 2016 35.55 - 53.33: 368 53.33 - 71.10: 66 71.10 - 88.88: 11 Dihedral angle restraints: 16005 sinusoidal: 6743 harmonic: 9262 Sorted by residual: dihedral pdb=" CA GLU H 170 " pdb=" C GLU H 170 " pdb=" N LEU H 171 " pdb=" CA LEU H 171 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLU C 170 " pdb=" C GLU C 170 " pdb=" N LEU C 171 " pdb=" CA LEU C 171 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU D 164 " pdb=" C LEU D 164 " pdb=" N PRO D 165 " pdb=" CA PRO D 165 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 16002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1955 0.039 - 0.079: 1516 0.079 - 0.118: 327 0.118 - 0.158: 90 0.158 - 0.197: 28 Chirality restraints: 3916 Sorted by residual: chirality pdb=" C2 PA8 G 305 " pdb=" C1 PA8 G 305 " pdb=" C3 PA8 G 305 " pdb=" O7 PA8 G 305 " both_signs ideal model delta sigma weight residual False -2.37 -2.57 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CB VAL F 156 " pdb=" CA VAL F 156 " pdb=" CG1 VAL F 156 " pdb=" CG2 VAL F 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL E 156 " pdb=" CA VAL E 156 " pdb=" CG1 VAL E 156 " pdb=" CG2 VAL E 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 3913 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 110 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO J 111 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 110 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO F 111 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 111 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 111 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 145 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO G 146 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 146 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 146 " -0.037 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8948 2.84 - 3.36: 20597 3.36 - 3.87: 39031 3.87 - 4.39: 47826 4.39 - 4.90: 81830 Nonbonded interactions: 198232 Sorted by model distance: nonbonded pdb=" O GLU B 126 " pdb=" OG SER B 130 " model vdw 2.328 3.040 nonbonded pdb=" O GLU E 126 " pdb=" OG SER E 130 " model vdw 2.350 3.040 nonbonded pdb=" O GLU H 126 " pdb=" OG SER H 130 " model vdw 2.351 3.040 nonbonded pdb=" O GLU I 126 " pdb=" OG SER I 130 " model vdw 2.357 3.040 nonbonded pdb=" O GLU A 126 " pdb=" OG SER A 130 " model vdw 2.360 3.040 ... (remaining 198227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.190 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.010 0.084 27335 Z= 0.457 Angle : 1.276 11.024 36839 Z= 0.550 Chirality : 0.054 0.197 3916 Planarity : 0.007 0.070 4499 Dihedral : 16.377 88.879 9900 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.14 % Allowed : 5.87 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.00 (0.08), residues: 3146 helix: -4.89 (0.03), residues: 2277 sheet: None (None), residues: 0 loop : -3.00 (0.16), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 240 TYR 0.016 0.002 TYR J 125 PHE 0.014 0.002 PHE E 254 TRP 0.023 0.003 TRP H 262 HIS 0.005 0.001 HIS K 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.46 (27302) covalent geometry : angle 1.27251 / 0.55 (36773) SS BOND : bond 0.00533 / 0.34 ( 33) SS BOND : angle 2.49358 / 1.69 ( 66) hydrogen bonds : bond 0.37814 / 24.33 ( 1093) hydrogen bonds : angle 10.42628 / 7.15 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 570 time to evaluate : 0.906 Fit side-chains REVERT: A 72 ARG cc_start: 0.8325 (ptp-170) cc_final: 0.7920 (ptm160) REVERT: A 169 GLU cc_start: 0.8320 (tp30) cc_final: 0.7931 (tp30) REVERT: A 204 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7746 (mtp-110) REVERT: A 232 ASP cc_start: 0.7693 (t70) cc_final: 0.7448 (m-30) REVERT: A 248 ASN cc_start: 0.8363 (t0) cc_final: 0.8073 (t0) REVERT: B 40 LYS cc_start: 0.8245 (ptpp) cc_final: 0.7770 (pttp) REVERT: B 204 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7702 (mtp85) REVERT: B 223 LYS cc_start: 0.7936 (mttp) cc_final: 0.7679 (mtpt) REVERT: B 232 ASP cc_start: 0.7797 (t70) cc_final: 0.7565 (m-30) REVERT: B 248 ASN cc_start: 0.8450 (t0) cc_final: 0.8136 (t0) REVERT: B 263 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7434 (mm-30) REVERT: C 44 SER cc_start: 0.8732 (m) cc_final: 0.8503 (p) REVERT: C 176 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7827 (mt0) REVERT: C 196 LEU cc_start: 0.8664 (tp) cc_final: 0.8405 (tt) REVERT: C 248 ASN cc_start: 0.8423 (t0) cc_final: 0.8142 (t0) REVERT: D 196 LEU cc_start: 0.8705 (tp) cc_final: 0.8497 (tt) REVERT: D 223 LYS cc_start: 0.7930 (mttp) cc_final: 0.7718 (mtpt) REVERT: D 232 ASP cc_start: 0.7891 (t70) cc_final: 0.7665 (m-30) REVERT: D 248 ASN cc_start: 0.8424 (t0) cc_final: 0.8126 (t0) REVERT: D 263 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7433 (mm-30) REVERT: E 40 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7892 (ptpp) REVERT: E 72 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.8237 (ptm160) REVERT: E 143 LYS cc_start: 0.8338 (tptt) cc_final: 0.7908 (tppt) REVERT: E 151 GLU cc_start: 0.7849 (mp0) cc_final: 0.7364 (mp0) REVERT: E 196 LEU cc_start: 0.8676 (tp) cc_final: 0.8424 (tt) REVERT: E 204 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7729 (mtp-110) REVERT: E 248 ASN cc_start: 0.8333 (t0) cc_final: 0.8050 (t0) REVERT: F 40 LYS cc_start: 0.8099 (ptpp) cc_final: 0.7773 (ptpp) REVERT: F 223 LYS cc_start: 0.8181 (mttp) cc_final: 0.7933 (mtpt) REVERT: F 248 ASN cc_start: 0.8439 (t0) cc_final: 0.8129 (t0) REVERT: G 16 THR cc_start: 0.8149 (t) cc_final: 0.7938 (m) REVERT: G 102 GLN cc_start: 0.7987 (tt0) cc_final: 0.7543 (tt0) REVERT: G 176 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7785 (mt0) REVERT: G 204 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7812 (mtp85) REVERT: G 232 ASP cc_start: 0.7537 (t70) cc_final: 0.7304 (t70) REVERT: G 248 ASN cc_start: 0.8586 (t0) cc_final: 0.8276 (t0) REVERT: H 156 VAL cc_start: 0.9288 (p) cc_final: 0.9069 (m) REVERT: H 204 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7698 (mtp85) REVERT: H 223 LYS cc_start: 0.8199 (mttp) cc_final: 0.7879 (mtpt) REVERT: H 248 ASN cc_start: 0.8311 (t0) cc_final: 0.8020 (t0) REVERT: H 263 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7470 (mm-30) REVERT: I 40 LYS cc_start: 0.8384 (ptpp) cc_final: 0.7884 (pttm) REVERT: I 72 ARG cc_start: 0.8470 (ptp-170) cc_final: 0.8192 (ptm160) REVERT: I 196 LEU cc_start: 0.8646 (tp) cc_final: 0.8386 (tt) REVERT: I 204 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7712 (mtp-110) REVERT: I 248 ASN cc_start: 0.8416 (t0) cc_final: 0.8134 (t0) REVERT: J 40 LYS cc_start: 0.8165 (ptpp) cc_final: 0.7888 (ttmm) REVERT: J 204 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7828 (mtp85) REVERT: J 232 ASP cc_start: 0.7682 (t70) cc_final: 0.7397 (t0) REVERT: J 248 ASN cc_start: 0.8411 (t0) cc_final: 0.8123 (t0) REVERT: K 40 LYS cc_start: 0.8295 (ptpp) cc_final: 0.7855 (pttm) REVERT: K 72 ARG cc_start: 0.8345 (ptp-170) cc_final: 0.8128 (ptm160) REVERT: K 204 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7813 (mtp85) REVERT: K 248 ASN cc_start: 0.8474 (t0) cc_final: 0.8235 (t0) REVERT: K 286 ASP cc_start: 0.8614 (m-30) cc_final: 0.8292 (m-30) outliers start: 4 outliers final: 3 residues processed: 571 average time/residue: 0.7287 time to fit residues: 472.7309 Evaluate side-chains 417 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 414 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain I residue 121 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 102 GLN A 287 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 225 GLN B 287 ASN C 102 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 273 GLN C 287 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 121 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 102 GLN E 121 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN F 102 GLN F 168 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN G 287 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN H 102 GLN H 121 ASN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN H 287 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 287 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN K 102 GLN K 121 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 GLN K 287 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119561 restraints weight = 30144.057| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.27 r_work: 0.3205 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27335 Z= 0.115 Angle : 0.553 12.515 36839 Z= 0.289 Chirality : 0.037 0.162 3916 Planarity : 0.005 0.052 4499 Dihedral : 10.649 59.901 3988 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.54 % Allowed : 13.67 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.12), residues: 3146 helix: -2.98 (0.08), residues: 2233 sheet: None (None), residues: 0 loop : -1.93 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 240 TYR 0.016 0.001 TYR E 98 PHE 0.010 0.001 PHE E 67 TRP 0.017 0.001 TRP E 60 HIS 0.002 0.000 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27302) covalent geometry : angle 0.55099 / 0.29 (36773) SS BOND : bond 0.00205 / 0.13 ( 33) SS BOND : angle 1.19380 / 0.83 ( 66) hydrogen bonds : bond 0.05350 / 3.46 ( 1093) hydrogen bonds : angle 4.15091 / 2.87 ( 3159) *********************** 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 454 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 411 time to evaluate : 1.016 Fit side-chains REVERT: A 72 ARG cc_start: 0.8833 (ptp-170) cc_final: 0.8384 (ptm160) REVERT: A 169 GLU cc_start: 0.8586 (tp30) cc_final: 0.8199 (tp30) REVERT: A 204 ARG cc_start: 0.8507 (mtp180) cc_final: 0.8092 (mtp-110) REVERT: A 232 ASP cc_start: 0.7846 (t70) cc_final: 0.7503 (m-30) REVERT: A 248 ASN cc_start: 0.7908 (t0) cc_final: 0.7664 (t0) REVERT: B 40 LYS cc_start: 0.8468 (ptpp) cc_final: 0.7996 (pttp) REVERT: B 232 ASP cc_start: 0.7866 (t70) cc_final: 0.7536 (m-30) REVERT: B 248 ASN cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: C 204 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7566 (mtp-110) REVERT: C 276 GLN cc_start: 0.8122 (pt0) cc_final: 0.7775 (pt0) REVERT: D 30 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7620 (m) REVERT: D 40 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8440 (ttmm) REVERT: D 65 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8482 (tp) REVERT: D 204 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8400 (mmm160) REVERT: D 220 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7903 (tm-30) REVERT: D 223 LYS cc_start: 0.8195 (mttp) cc_final: 0.7922 (mtpt) REVERT: D 232 ASP cc_start: 0.7983 (t70) cc_final: 0.7689 (m-30) REVERT: E 40 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8023 (pttp) REVERT: E 143 LYS cc_start: 0.8320 (tptt) cc_final: 0.7903 (tppt) REVERT: E 248 ASN cc_start: 0.8116 (t0) cc_final: 0.7901 (t0) REVERT: E 273 GLN cc_start: 0.8274 (pt0) cc_final: 0.8055 (mt0) REVERT: F 40 LYS cc_start: 0.8355 (ptpp) cc_final: 0.8064 (ptpp) REVERT: F 248 ASN cc_start: 0.8086 (t0) cc_final: 0.7847 (t0) REVERT: G 46 GLU cc_start: 0.6635 (pt0) cc_final: 0.6364 (pp20) REVERT: G 102 GLN cc_start: 0.7737 (tt0) cc_final: 0.7460 (tt0) REVERT: G 204 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8395 (mtp85) REVERT: G 232 ASP cc_start: 0.7906 (t70) cc_final: 0.7648 (m-30) REVERT: G 248 ASN cc_start: 0.8191 (t0) cc_final: 0.7969 (t0) REVERT: H 151 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: H 232 ASP cc_start: 0.8149 (m-30) cc_final: 0.7821 (m-30) REVERT: H 248 ASN cc_start: 0.8239 (t0) cc_final: 0.7994 (t0) REVERT: I 40 LYS cc_start: 0.8509 (ptpp) cc_final: 0.8045 (pttp) REVERT: I 273 GLN cc_start: 0.8434 (pt0) cc_final: 0.8210 (mt0) REVERT: J 40 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8260 (ttmm) REVERT: J 204 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8329 (mtp85) REVERT: J 248 ASN cc_start: 0.7858 (t0) cc_final: 0.7653 (t0) REVERT: K 16 THR cc_start: 0.8296 (m) cc_final: 0.8076 (m) REVERT: K 40 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8059 (pttp) REVERT: K 248 ASN cc_start: 0.8342 (t0) cc_final: 0.8125 (t0) outliers start: 43 outliers final: 13 residues processed: 430 average time/residue: 0.6743 time to fit residues: 334.1188 Evaluate side-chains 356 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 339 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 258 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 HIS ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 121 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115140 restraints weight = 30274.921| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.29 r_work: 0.3150 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 27335 Z= 0.236 Angle : 0.641 10.245 36839 Z= 0.324 Chirality : 0.043 0.188 3916 Planarity : 0.005 0.040 4499 Dihedral : 10.773 59.954 3982 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.26 % Allowed : 14.53 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.14), residues: 3146 helix: -1.88 (0.10), residues: 2244 sheet: None (None), residues: 0 loop : -1.59 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.013 0.002 TYR I 218 PHE 0.009 0.001 PHE E 192 TRP 0.013 0.002 TRP H 262 HIS 0.004 0.001 HIS F 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (27302) covalent geometry : angle 0.63739 / 0.32 (36773) SS BOND : bond 0.00539 / 0.34 ( 33) SS BOND : angle 1.68513 / 1.14 ( 66) hydrogen bonds : bond 0.06590 / 4.27 ( 1093) hydrogen bonds : angle 3.77964 / 2.62 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6292 Ramachandran restraints generated. 3146 Oldfield, 0 Emsley, 3146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 353 time to evaluate : 1.023 Fit side-chains REVERT: A 72 ARG cc_start: 0.8796 (ptp-170) cc_final: 0.8397 (ptm-80) REVERT: A 169 GLU cc_start: 0.8580 (tp30) cc_final: 0.8172 (tp30) REVERT: A 204 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8066 (mtp-110) REVERT: A 232 ASP cc_start: 0.7908 (t70) cc_final: 0.7465 (m-30) REVERT: A 248 ASN cc_start: 0.8041 (t0) cc_final: 0.7786 (t0) REVERT: B 40 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8011 (pttp) REVERT: B 71 ASN cc_start: 0.8803 (t0) cc_final: 0.8523 (m-40) REVERT: B 232 ASP cc_start: 0.7939 (t70) cc_final: 0.7537 (m-30) REVERT: C 46 GLU cc_start: 0.7600 (pp20) cc_final: 0.6997 (pp20) REVERT: C 85 ARG cc_start: 0.6818 (mmp-170) cc_final: 0.6555 (mmm-85) REVERT: D 40 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8473 (ttmm) REVERT: D 220 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7835 (tm-30) REVERT: D 223 LYS cc_start: 0.8166 (mttp) cc_final: 0.7893 (mtpt) REVERT: D 232 ASP cc_start: 0.8108 (t70) cc_final: 0.7626 (m-30) REVERT: E 40 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8128 (pttp) REVERT: E 143 LYS cc_start: 0.8332 (tptt) cc_final: 0.7921 (tppt) REVERT: E 248 ASN cc_start: 0.8160 (t0) cc_final: 0.7958 (t0) REVERT: F 40 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8120 (ttmm) REVERT: F 248 ASN cc_start: 0.8387 (t0) cc_final: 0.8136 (t0) REVERT: G 102 GLN cc_start: 0.7816 (tt0) cc_final: 0.7576 (tt0) REVERT: G 248 ASN cc_start: 0.8309 (t0) cc_final: 0.8091 (t0) REVERT: H 176 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: H 248 ASN cc_start: 0.8337 (t0) cc_final: 0.8114 (t0) REVERT: I 40 LYS cc_start: 0.8674 (ptpp) cc_final: 0.8184 (pttp) REVERT: I 151 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: I 273 GLN cc_start: 0.8417 (pt0) cc_final: 0.8187 (mt0) REVERT: J 40 LYS cc_start: 0.8675 (ptpp) cc_final: 0.8341 (ttmm) REVERT: J 113 MET cc_start: 0.9157 (ttp) cc_final: 0.8772 (ttm) REVERT: J 204 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8320 (mtp85) REVERT: J 248 ASN cc_start: 0.8218 (t0) cc_final: 0.8001 (t0) REVERT: K 40 LYS cc_start: 0.8638 (ptpp) cc_final: 0.8148 (pttp) REVERT: K 151 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: K 248 ASN cc_start: 0.8446 (t0) cc_final: 0.8213 (t0) outliers start: 91 outliers final: 52 residues processed: 415 average time/residue: 0.6675 time to fit residues: 321.1678 Evaluate side-chains 383 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 151 GLU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 258 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 65 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 156 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN K 154 HIS ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118868 restraints weight = 29920.791| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27335 Z= 0.114 Angle : 0.534 14.351 36839 Z= 0.267 Chirality : 0.037 0.176 3916 Planarity : 0.004 0.049 4499 Dihedral : 10.061 59.852 3982 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 16.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 3146 helix: -1.13 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.011 0.001 TYR E 98 PHE 0.020 0.001 PHE E 88 TRP 0.009 0.001 TRP H 60 HIS 0.002 0.001 HIS H 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (27302) covalent geometry : angle 0.53260 / 0.27 (36773) SS BOND : bond 0.00261 / 0.16 ( 33) SS BOND : angle 1.10362 / 0.77 ( 66) hydrogen bonds : bond 0.04294 / 2.78 ( 1093) hydrogen bonds : angle 3.32858 / 2.30 ( 3159) *********************** 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 432 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 353 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8758 (ptp-170) cc_final: 0.8310 (ptm160) REVERT: A 169 GLU cc_start: 0.8570 (tp30) cc_final: 0.8209 (tp30) REVERT: A 204 ARG cc_start: 0.8428 (mtp180) cc_final: 0.7991 (mtp-110) REVERT: A 232 ASP cc_start: 0.7754 (t70) cc_final: 0.7427 (m-30) REVERT: A 248 ASN cc_start: 0.7936 (t0) cc_final: 0.7696 (t0) REVERT: B 40 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (pttp) REVERT: B 176 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7807 (tt0) REVERT: B 232 ASP cc_start: 0.7814 (t70) cc_final: 0.7465 (m-30) REVERT: B 248 ASN cc_start: 0.8216 (t0) cc_final: 0.7983 (t0) REVERT: C 30 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7632 (m) REVERT: C 46 GLU cc_start: 0.7709 (pp20) cc_final: 0.6936 (pp20) REVERT: C 85 ARG cc_start: 0.6843 (mmp-170) cc_final: 0.6576 (mmm-85) REVERT: C 151 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: C 250 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7769 (mmp-170) REVERT: C 276 GLN cc_start: 0.8171 (pt0) cc_final: 0.7894 (pt0) REVERT: D 220 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7906 (tm-30) REVERT: D 232 ASP cc_start: 0.7990 (t70) cc_final: 0.7624 (m-30) REVERT: E 40 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8074 (pttp) REVERT: E 143 LYS cc_start: 0.8257 (tptt) cc_final: 0.7865 (tppt) REVERT: E 248 ASN cc_start: 0.8066 (t0) cc_final: 0.7861 (t0) REVERT: E 273 GLN cc_start: 0.8165 (pt0) cc_final: 0.7919 (mt0) REVERT: F 40 LYS cc_start: 0.8379 (ptpp) cc_final: 0.8130 (ttmm) REVERT: F 169 GLU cc_start: 0.8340 (tp30) cc_final: 0.7599 (tp30) REVERT: F 248 ASN cc_start: 0.8153 (t0) cc_final: 0.7936 (t0) REVERT: G 102 GLN cc_start: 0.7677 (tt0) cc_final: 0.7439 (tt0) REVERT: G 248 ASN cc_start: 0.8234 (t0) cc_final: 0.8026 (t0) REVERT: H 248 ASN cc_start: 0.8341 (t0) cc_final: 0.8093 (t0) REVERT: I 40 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8015 (pttp) REVERT: I 196 LEU cc_start: 0.8170 (tp) cc_final: 0.7950 (tt) REVERT: J 72 ARG cc_start: 0.8707 (ptp-170) cc_final: 0.8289 (ptm160) REVERT: J 113 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8509 (ttm) REVERT: J 204 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8302 (mtp85) REVERT: K 11 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6311 (t80) REVERT: K 40 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8025 (pttp) REVERT: K 151 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: K 248 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0) outliers start: 79 outliers final: 36 residues processed: 408 average time/residue: 0.6240 time to fit residues: 296.4524 Evaluate side-chains 359 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 315 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 113 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 151 GLU Chi-restraints excluded: chain K residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 294 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 GLN K 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120379 restraints weight = 29567.268| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.08 r_work: 0.3217 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27335 Z= 0.107 Angle : 0.527 14.673 36839 Z= 0.262 Chirality : 0.037 0.179 3916 Planarity : 0.003 0.057 4499 Dihedral : 9.486 59.938 3982 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.22 % Allowed : 17.04 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 3146 helix: -0.63 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 240 TYR 0.010 0.001 TYR C 98 PHE 0.017 0.001 PHE H 88 TRP 0.008 0.001 TRP H 262 HIS 0.002 0.000 HIS H 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (27302) covalent geometry : angle 0.52572 / 0.26 (36773) SS BOND : bond 0.00242 / 0.15 ( 33) SS BOND : angle 0.97444 / 0.68 ( 66) hydrogen bonds : bond 0.03989 / 2.59 ( 1093) hydrogen bonds : angle 3.13258 / 2.16 ( 3159) *********************** 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 442 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 352 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 11 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 40 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8266 (tptt) REVERT: A 72 ARG cc_start: 0.8735 (ptp-170) cc_final: 0.8322 (ptm160) REVERT: A 169 GLU cc_start: 0.8530 (tp30) cc_final: 0.8183 (tp30) REVERT: A 204 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8270 (mtp-110) REVERT: A 232 ASP cc_start: 0.7907 (t70) cc_final: 0.7602 (m-30) REVERT: A 248 ASN cc_start: 0.8005 (t0) cc_final: 0.7789 (t0) REVERT: B 40 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7985 (pttp) REVERT: B 68 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7383 (t80) REVERT: B 232 ASP cc_start: 0.7943 (t70) cc_final: 0.7613 (m-30) REVERT: C 30 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8057 (m) REVERT: C 46 GLU cc_start: 0.7663 (pp20) cc_final: 0.7055 (pp20) REVERT: C 72 ARG cc_start: 0.8743 (ptp-170) cc_final: 0.8486 (ptm-80) REVERT: C 85 ARG cc_start: 0.6919 (mmp-170) cc_final: 0.6703 (mmm-85) REVERT: C 250 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7767 (mmp-170) REVERT: C 276 GLN cc_start: 0.8247 (pt0) cc_final: 0.7970 (pt0) REVERT: D 65 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8541 (tp) REVERT: D 151 GLU cc_start: 0.7937 (mp0) cc_final: 0.7597 (mm-30) REVERT: D 176 GLN cc_start: 0.8323 (mt0) cc_final: 0.8084 (mt0) REVERT: D 232 ASP cc_start: 0.8065 (t70) cc_final: 0.7793 (m-30) REVERT: E 16 THR cc_start: 0.8302 (t) cc_final: 0.8091 (m) REVERT: E 40 LYS cc_start: 0.8487 (ptpp) cc_final: 0.8128 (pttp) REVERT: E 68 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7544 (t80) REVERT: E 143 LYS cc_start: 0.8260 (tptt) cc_final: 0.7847 (tppt) REVERT: F 151 GLU cc_start: 0.8016 (mp0) cc_final: 0.7633 (mm-30) REVERT: F 169 GLU cc_start: 0.8418 (tp30) cc_final: 0.7924 (tp30) REVERT: F 248 ASN cc_start: 0.8189 (t0) cc_final: 0.7971 (t0) REVERT: G 40 LYS cc_start: 0.8116 (pttp) cc_final: 0.7829 (ttmm) REVERT: G 113 MET cc_start: 0.8712 (mtp) cc_final: 0.8470 (ttm) REVERT: G 248 ASN cc_start: 0.8265 (t0) cc_final: 0.8055 (t0) REVERT: H 68 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7439 (t80) REVERT: H 248 ASN cc_start: 0.8358 (t0) cc_final: 0.8145 (t0) REVERT: I 11 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6412 (t80) REVERT: I 40 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8070 (ptpp) REVERT: I 113 MET cc_start: 0.8680 (mtp) cc_final: 0.8448 (ttm) REVERT: I 196 LEU cc_start: 0.8294 (tp) cc_final: 0.8086 (tt) REVERT: J 72 ARG cc_start: 0.8749 (ptp-170) cc_final: 0.8383 (ptm160) REVERT: J 204 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8306 (mtp85) REVERT: K 11 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6396 (t80) REVERT: K 40 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8010 (pttp) REVERT: K 102 GLN cc_start: 0.7599 (tt0) cc_final: 0.7244 (tt0) REVERT: K 232 ASP cc_start: 0.8151 (t0) cc_final: 0.7922 (m-30) outliers start: 90 outliers final: 44 residues processed: 419 average time/residue: 0.6225 time to fit residues: 304.0047 Evaluate side-chains 373 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 318 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 258 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 279 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 237 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 224 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 176 GLN H 154 HIS ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN K 168 ASN K 220 GLN K 228 ASN K 277 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120804 restraints weight = 29698.959| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.07 r_work: 0.3223 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27335 Z= 0.103 Angle : 0.520 14.926 36839 Z= 0.255 Chirality : 0.037 0.179 3916 Planarity : 0.004 0.063 4499 Dihedral : 9.142 59.790 3982 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.36 % Allowed : 17.54 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 3146 helix: -0.17 (0.11), residues: 2255 sheet: None (None), residues: 0 loop : -0.97 (0.23), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.011 0.001 TYR E 98 PHE 0.024 0.001 PHE E 88 TRP 0.007 0.001 TRP H 60 HIS 0.002 0.000 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (27302) covalent geometry : angle 0.51919 / 0.26 (36773) SS BOND : bond 0.00227 / 0.14 ( 33) SS BOND : angle 0.90640 / 0.64 ( 66) hydrogen bonds : bond 0.03770 / 2.45 ( 1093) hydrogen bonds : angle 3.04341 / 2.10 ( 3159) *********************** 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 407 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 313 time to evaluate : 0.906 Fit side-chains REVERT: A 11 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6313 (t80) REVERT: A 40 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8267 (tptt) REVERT: A 169 GLU cc_start: 0.8477 (tp30) cc_final: 0.8127 (tp30) REVERT: A 232 ASP cc_start: 0.7963 (t70) cc_final: 0.7641 (m-30) REVERT: A 248 ASN cc_start: 0.7989 (t0) cc_final: 0.7777 (t0) REVERT: B 11 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6054 (t80) REVERT: B 40 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8040 (ptpp) REVERT: B 68 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 232 ASP cc_start: 0.7937 (t70) cc_final: 0.7599 (m-30) REVERT: C 30 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (m) REVERT: C 46 GLU cc_start: 0.7644 (pp20) cc_final: 0.7035 (pp20) REVERT: C 276 GLN cc_start: 0.8252 (pt0) cc_final: 0.8001 (pt0) REVERT: D 151 GLU cc_start: 0.7927 (mp0) cc_final: 0.7642 (mm-30) REVERT: D 232 ASP cc_start: 0.8059 (t70) cc_final: 0.7766 (m-30) REVERT: E 40 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: E 68 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7669 (t80) REVERT: F 151 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: F 169 GLU cc_start: 0.8396 (tp30) cc_final: 0.7897 (tp30) REVERT: F 248 ASN cc_start: 0.8163 (t0) cc_final: 0.7944 (t0) REVERT: F 276 GLN cc_start: 0.8256 (pt0) cc_final: 0.7793 (mt0) REVERT: G 40 LYS cc_start: 0.8066 (pttp) cc_final: 0.7857 (ttmm) REVERT: G 248 ASN cc_start: 0.8258 (t0) cc_final: 0.8047 (t0) REVERT: H 68 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7485 (t80) REVERT: H 248 ASN cc_start: 0.8359 (t0) cc_final: 0.8147 (t0) REVERT: I 11 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6285 (t80) REVERT: I 40 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8051 (pttp) REVERT: I 196 LEU cc_start: 0.8291 (tp) cc_final: 0.8084 (tt) REVERT: J 68 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7647 (t80) REVERT: J 72 ARG cc_start: 0.8737 (ptp-170) cc_final: 0.8360 (ptm160) REVERT: J 204 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8357 (mtp85) REVERT: J 273 GLN cc_start: 0.8261 (pt0) cc_final: 0.8007 (mt0) REVERT: K 11 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6421 (t80) REVERT: K 151 GLU cc_start: 0.8126 (tp30) cc_final: 0.7903 (mp0) REVERT: K 232 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: K 276 GLN cc_start: 0.8234 (pt0) cc_final: 0.7934 (mt0) outliers start: 94 outliers final: 50 residues processed: 383 average time/residue: 0.5860 time to fit residues: 264.2615 Evaluate side-chains 367 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 256 MET Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 121 ASN Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 258 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 140 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 280 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 GLN K 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121617 restraints weight = 29505.560| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.07 r_work: 0.3233 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27335 Z= 0.096 Angle : 0.519 14.190 36839 Z= 0.255 Chirality : 0.037 0.181 3916 Planarity : 0.003 0.075 4499 Dihedral : 8.843 59.441 3982 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.90 % Allowed : 18.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 3146 helix: 0.41 (0.12), residues: 2156 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.012 0.001 TYR C 98 PHE 0.023 0.001 PHE E 88 TRP 0.007 0.001 TRP H 60 HIS 0.002 0.000 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (27302) covalent geometry : angle 0.51821 / 0.25 (36773) SS BOND : bond 0.00219 / 0.14 ( 33) SS BOND : angle 0.85736 / 0.61 ( 66) hydrogen bonds : bond 0.03501 / 2.27 ( 1093) hydrogen bonds : angle 2.98185 / 2.05 ( 3159) *********************** 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 385 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 304 time to evaluate : 0.991 Fit side-chains REVERT: A 11 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6123 (t80) REVERT: A 40 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8253 (tptt) REVERT: A 68 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 169 GLU cc_start: 0.8427 (tp30) cc_final: 0.8043 (tp30) REVERT: A 232 ASP cc_start: 0.7960 (t70) cc_final: 0.7631 (m-30) REVERT: A 248 ASN cc_start: 0.7959 (t0) cc_final: 0.7748 (t0) REVERT: B 11 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6011 (t80) REVERT: B 40 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8045 (ptpp) REVERT: B 68 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 232 ASP cc_start: 0.7917 (t70) cc_final: 0.7635 (m-30) REVERT: C 30 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8095 (m) REVERT: C 46 GLU cc_start: 0.7624 (pp20) cc_final: 0.7030 (pp20) REVERT: C 151 GLU cc_start: 0.7862 (mp0) cc_final: 0.7578 (mm-30) REVERT: C 276 GLN cc_start: 0.8261 (pt0) cc_final: 0.8022 (pt0) REVERT: D 151 GLU cc_start: 0.7912 (mp0) cc_final: 0.7587 (mm-30) REVERT: D 232 ASP cc_start: 0.8046 (t70) cc_final: 0.7772 (m-30) REVERT: E 40 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8154 (ptpp) REVERT: E 68 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7688 (t80) REVERT: F 151 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: F 169 GLU cc_start: 0.8367 (tp30) cc_final: 0.7631 (tp30) REVERT: F 248 ASN cc_start: 0.8141 (t0) cc_final: 0.7928 (t0) REVERT: F 276 GLN cc_start: 0.8248 (pt0) cc_final: 0.7798 (mt0) REVERT: G 196 LEU cc_start: 0.8368 (tp) cc_final: 0.8094 (tp) REVERT: G 248 ASN cc_start: 0.8235 (t0) cc_final: 0.8026 (t0) REVERT: H 248 ASN cc_start: 0.8340 (t0) cc_final: 0.8129 (t0) REVERT: I 11 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6194 (t80) REVERT: I 40 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8014 (pttp) REVERT: J 68 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7463 (t80) REVERT: J 72 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8323 (ptm160) REVERT: J 204 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8350 (mtp85) REVERT: J 273 GLN cc_start: 0.8267 (pt0) cc_final: 0.8035 (mt0) REVERT: K 11 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6386 (t80) REVERT: K 151 GLU cc_start: 0.8103 (tp30) cc_final: 0.7896 (mp0) REVERT: K 232 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: K 276 GLN cc_start: 0.8203 (pt0) cc_final: 0.7917 (mt0) outliers start: 81 outliers final: 41 residues processed: 363 average time/residue: 0.5616 time to fit residues: 241.2804 Evaluate side-chains 355 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 158 CYS Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 258 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 204 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 0.0670 chunk 155 optimal weight: 0.0070 chunk 143 optimal weight: 0.5980 chunk 136 optimal weight: 0.0470 chunk 152 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 GLN C 154 HIS ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN H 273 GLN I 168 ASN K 121 ASN K 228 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.165248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124173 restraints weight = 29653.893| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.06 r_work: 0.3258 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27335 Z= 0.082 Angle : 0.495 15.538 36839 Z= 0.242 Chirality : 0.035 0.176 3916 Planarity : 0.003 0.060 4499 Dihedral : 8.207 59.845 3982 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.65 % Allowed : 18.83 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 3146 helix: 0.65 (0.12), residues: 2222 sheet: None (None), residues: 0 loop : -0.88 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.012 0.001 TYR C 98 PHE 0.017 0.000 PHE H 88 TRP 0.007 0.001 TRP H 150 HIS 0.002 0.000 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.08 (27302) covalent geometry : angle 0.49475 / 0.24 (36773) SS BOND : bond 0.00176 / 0.11 ( 33) SS BOND : angle 0.66356 / 0.49 ( 66) hydrogen bonds : bond 0.02773 / 1.80 ( 1093) hydrogen bonds : angle 2.86339 / 1.97 ( 3159) *********************** 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 387 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 313 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 11 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.5962 (t80) REVERT: A 34 PHE cc_start: 0.7595 (m-80) cc_final: 0.7325 (m-10) REVERT: A 40 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8201 (tptt) REVERT: A 68 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7556 (t80) REVERT: A 169 GLU cc_start: 0.8447 (tp30) cc_final: 0.8083 (tp30) REVERT: A 232 ASP cc_start: 0.7887 (t70) cc_final: 0.7605 (m-30) REVERT: A 248 ASN cc_start: 0.7906 (t0) cc_final: 0.7670 (t0) REVERT: B 11 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5799 (t80) REVERT: B 40 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8003 (ptpp) REVERT: B 68 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7387 (t80) REVERT: B 232 ASP cc_start: 0.7814 (t70) cc_final: 0.7569 (m-30) REVERT: C 151 GLU cc_start: 0.7868 (mp0) cc_final: 0.7599 (mm-30) REVERT: C 276 GLN cc_start: 0.8205 (pt0) cc_final: 0.7991 (pt0) REVERT: D 151 GLU cc_start: 0.7863 (mp0) cc_final: 0.7623 (mm-30) REVERT: D 232 ASP cc_start: 0.8012 (t70) cc_final: 0.7757 (m-30) REVERT: E 40 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8100 (ptpp) REVERT: E 68 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7549 (t80) REVERT: F 151 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: F 169 GLU cc_start: 0.8374 (tp30) cc_final: 0.7859 (tp30) REVERT: F 248 ASN cc_start: 0.8049 (t0) cc_final: 0.7843 (t0) REVERT: F 276 GLN cc_start: 0.8183 (pt0) cc_final: 0.7808 (mt0) REVERT: G 68 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7573 (t80) REVERT: G 196 LEU cc_start: 0.8337 (tp) cc_final: 0.8097 (tp) REVERT: G 224 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8018 (tt0) REVERT: G 232 ASP cc_start: 0.8028 (t0) cc_final: 0.7778 (m-30) REVERT: G 248 ASN cc_start: 0.8159 (t0) cc_final: 0.7951 (t0) REVERT: G 276 GLN cc_start: 0.7954 (pt0) cc_final: 0.7438 (mt0) REVERT: H 248 ASN cc_start: 0.8285 (t0) cc_final: 0.8060 (t0) REVERT: I 11 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6038 (t80) REVERT: I 32 ARG cc_start: 0.7246 (mmm160) cc_final: 0.7000 (tpt90) REVERT: I 40 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7922 (pttp) REVERT: I 169 GLU cc_start: 0.8622 (tp30) cc_final: 0.7964 (tp30) REVERT: J 68 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7454 (t80) REVERT: J 224 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8038 (tt0) REVERT: K 11 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6234 (t80) REVERT: K 224 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7631 (pt0) REVERT: K 276 GLN cc_start: 0.8075 (pt0) cc_final: 0.7811 (mt0) outliers start: 74 outliers final: 38 residues processed: 372 average time/residue: 0.5758 time to fit residues: 252.8326 Evaluate side-chains 341 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 PHE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 158 CYS Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 158 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 53 optimal weight: 0.0470 chunk 255 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 GLN D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 220 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN J 71 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123453 restraints weight = 29582.309| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.06 r_work: 0.3241 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27335 Z= 0.087 Angle : 0.504 15.055 36839 Z= 0.245 Chirality : 0.036 0.178 3916 Planarity : 0.003 0.057 4499 Dihedral : 8.006 59.829 3982 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.22 % Allowed : 19.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 3146 helix: 0.84 (0.12), residues: 2233 sheet: None (None), residues: 0 loop : -0.85 (0.23), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.012 0.001 TYR C 98 PHE 0.025 0.001 PHE E 88 TRP 0.007 0.001 TRP I 150 HIS 0.002 0.000 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (27302) covalent geometry : angle 0.50354 / 0.24 (36773) SS BOND : bond 0.00154 / 0.09 ( 33) SS BOND : angle 0.69134 / 0.50 ( 66) hydrogen bonds : bond 0.03082 / 2.00 ( 1093) hydrogen bonds : angle 2.84423 / 1.96 ( 3159) *********************** 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 356 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 34 PHE cc_start: 0.7569 (m-80) cc_final: 0.7292 (m-10) REVERT: A 40 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8217 (tptt) REVERT: A 68 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 85 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6573 (mmm-85) REVERT: A 169 GLU cc_start: 0.8401 (tp30) cc_final: 0.8105 (tp30) REVERT: A 232 ASP cc_start: 0.8019 (t70) cc_final: 0.7717 (m-30) REVERT: A 248 ASN cc_start: 0.7954 (t0) cc_final: 0.7745 (t0) REVERT: B 11 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.5822 (t80) REVERT: B 68 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 151 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: D 232 ASP cc_start: 0.8016 (t70) cc_final: 0.7748 (m-30) REVERT: E 40 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8083 (ptpp) REVERT: E 68 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7586 (t80) REVERT: F 151 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: F 169 GLU cc_start: 0.8392 (tp30) cc_final: 0.7774 (tp30) REVERT: F 248 ASN cc_start: 0.8023 (t0) cc_final: 0.7805 (t0) REVERT: F 276 GLN cc_start: 0.8188 (pt0) cc_final: 0.7831 (mt0) REVERT: G 68 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7697 (t80) REVERT: G 196 LEU cc_start: 0.8363 (tp) cc_final: 0.8112 (tp) REVERT: G 224 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7946 (pt0) REVERT: G 232 ASP cc_start: 0.8054 (t0) cc_final: 0.7774 (m-30) REVERT: G 276 GLN cc_start: 0.7948 (pt0) cc_final: 0.7415 (mt0) REVERT: H 248 ASN cc_start: 0.8260 (t0) cc_final: 0.8057 (t0) REVERT: I 40 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7915 (pttp) REVERT: I 169 GLU cc_start: 0.8609 (tp30) cc_final: 0.7940 (tp30) REVERT: J 68 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7452 (t80) REVERT: J 224 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8015 (tt0) REVERT: K 151 GLU cc_start: 0.7958 (mp0) cc_final: 0.7662 (mm-30) REVERT: K 224 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7644 (pt0) REVERT: K 276 GLN cc_start: 0.8075 (pt0) cc_final: 0.7832 (mt0) outliers start: 62 outliers final: 37 residues processed: 343 average time/residue: 0.5537 time to fit residues: 224.7341 Evaluate side-chains 337 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE 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 17 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 158 CYS Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 158 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 203 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 229 optimal weight: 0.0770 chunk 267 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN J 71 ASN J 168 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120439 restraints weight = 29511.094| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.07 r_work: 0.3212 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27335 Z= 0.116 Angle : 0.547 14.957 36839 Z= 0.264 Chirality : 0.038 0.183 3916 Planarity : 0.003 0.057 4499 Dihedral : 8.245 59.741 3982 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.08 % Allowed : 19.86 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3146 helix: 1.00 (0.12), residues: 2167 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.010 0.001 TYR C 98 PHE 0.025 0.001 PHE E 88 TRP 0.009 0.001 TRP H 150 HIS 0.002 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27302) covalent geometry : angle 0.54550 / 0.26 (36773) SS BOND : bond 0.00241 / 0.15 ( 33) SS BOND : angle 0.95452 / 0.67 ( 66) hydrogen bonds : bond 0.04003 / 2.60 ( 1093) hydrogen bonds : angle 2.94834 / 2.03 ( 3159) ********************** 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 362 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8285 (tptt) REVERT: A 68 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 85 ARG cc_start: 0.6954 (mmp-170) cc_final: 0.6692 (mmm-85) REVERT: A 169 GLU cc_start: 0.8390 (tp30) cc_final: 0.7998 (tp30) REVERT: A 232 ASP cc_start: 0.7990 (t70) cc_final: 0.7645 (m-30) REVERT: A 248 ASN cc_start: 0.7965 (t0) cc_final: 0.7745 (t0) REVERT: B 11 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5934 (t80) REVERT: B 68 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7450 (t80) REVERT: C 151 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: D 151 GLU cc_start: 0.7908 (mp0) cc_final: 0.7607 (mm-30) REVERT: D 232 ASP cc_start: 0.8129 (t70) cc_final: 0.7767 (m-30) REVERT: E 40 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8078 (ptpp) REVERT: E 68 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7630 (t80) REVERT: F 151 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: F 169 GLU cc_start: 0.8379 (tp30) cc_final: 0.7994 (tp30) REVERT: F 276 GLN cc_start: 0.8156 (pt0) cc_final: 0.7806 (mt0) REVERT: G 224 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7961 (pt0) REVERT: H 248 ASN cc_start: 0.8341 (t0) cc_final: 0.8139 (t0) REVERT: I 11 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5902 (t80) REVERT: I 40 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7973 (pttp) REVERT: J 68 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7605 (t80) REVERT: K 102 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: K 224 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7650 (pt0) REVERT: K 276 GLN cc_start: 0.8213 (pt0) cc_final: 0.7925 (mt0) outliers start: 58 outliers final: 39 residues processed: 350 average time/residue: 0.5795 time to fit residues: 239.2953 Evaluate side-chains 345 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 87 ILE 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 E residue 258 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 158 CYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 158 CYS Chi-restraints excluded: chain J residue 258 THR Chi-restraints excluded: chain K residue 102 GLN Chi-restraints excluded: chain K residue 158 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 192 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 4 optimal weight: 0.0010 chunk 71 optimal weight: 5.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119301 restraints weight = 29481.776| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.07 r_work: 0.3188 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27335 Z= 0.139 Angle : 0.576 14.843 36839 Z= 0.276 Chirality : 0.040 0.186 3916 Planarity : 0.004 0.058 4499 Dihedral : 8.455 59.928 3982 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.25 % Allowed : 19.86 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 3146 helix: 0.72 (0.12), residues: 2244 sheet: None (None), residues: 0 loop : -0.68 (0.24), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 32 TYR 0.011 0.001 TYR C 98 PHE 0.026 0.001 PHE E 88 TRP 0.009 0.001 TRP E 150 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (27302) covalent geometry : angle 0.57475 / 0.28 (36773) SS BOND : bond 0.00282 / 0.17 ( 33) SS BOND : angle 1.06151 / 0.74 ( 66) hydrogen bonds : bond 0.04383 / 2.84 ( 1093) hydrogen bonds : angle 3.02168 / 2.08 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7678.63 seconds wall clock time: 144 minutes 54.26 seconds (8694.26 seconds total)