Starting phenix.real_space_refine on Fri Feb 6 00:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.cif Found real_map, /net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9me1_48182/02_2026/9me1_48182.map" } resolution = 3.37 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= 0.002 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 13988 2.51 5 N 3479 2.21 5 O 3560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21155 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "A" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2277 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "N" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "O" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "E" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "K" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "L" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "M" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "J" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 363 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 4.95, per 1000 atoms: 0.23 Number of scatterers: 21155 At special positions: 0 Unit cell: (99.946, 99.946, 167.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3560 8.00 N 3479 7.00 C 13988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 11 " distance=2.03 Simple disulfide: pdb=" SG CYS O 9 " - pdb=" SG CYS O 11 " distance=2.04 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS I 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 109 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS K 109 " - pdb=" SG CYS K 186 " distance=2.03 Simple disulfide: pdb=" SG CYS L 109 " - pdb=" SG CYS L 186 " distance=2.03 Simple disulfide: pdb=" SG CYS P 9 " - pdb=" SG CYS P 11 " distance=2.05 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 11 " distance=2.04 Simple disulfide: pdb=" SG CYS J 9 " - pdb=" SG CYS J 11 " distance=2.05 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 11 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 11 " distance=2.03 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 11 " distance=2.03 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: 1.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5358 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 68.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 34 through 64 removed outlier: 3.812A pdb=" N LYS B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 39 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 72 through 100 removed outlier: 4.513A pdb=" N TYR B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 104 through 140 removed outlier: 4.220A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 155 through 167 removed outlier: 4.690A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 192 through 227 removed outlier: 3.666A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.649A pdb=" N SER B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.087A pdb=" N ARG B 235 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 266 removed outlier: 4.102A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.631A pdb=" N ILE B 300 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 64 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 100 removed outlier: 4.242A pdb=" N TYR A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.977A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 139 removed outlier: 3.977A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 167 removed outlier: 5.437A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.658A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 237 through 267 removed outlier: 3.978A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 272 through 291 removed outlier: 4.171A pdb=" N PHE A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'N' and resid 55 through 64 Processing helix chain 'O' and resid 55 through 64 Processing helix chain 'C' and resid 36 through 64 Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.775A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 104 through 139 removed outlier: 4.208A pdb=" N LEU C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 155 through 167 removed outlier: 4.735A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 226 removed outlier: 3.682A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.195A pdb=" N ARG C 235 " --> pdb=" O HIS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 266 removed outlier: 4.061A pdb=" N THR C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 274 through 291 Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.620A pdb=" N ILE C 300 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 64 removed outlier: 3.647A pdb=" N ILE D 39 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 72 through 100 removed outlier: 4.445A pdb=" N TYR D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Proline residue: D 92 - end of helix Processing helix chain 'D' and resid 104 through 139 removed outlier: 4.213A pdb=" N LEU D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 154 through 167 removed outlier: 4.427A pdb=" N VAL D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 192 through 227 removed outlier: 3.675A pdb=" N VAL D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 3.673A pdb=" N SER D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.184A pdb=" N ARG D 235 " --> pdb=" O HIS D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 266 removed outlier: 4.091A pdb=" N THR D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 274 through 291 Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.596A pdb=" N ILE D 300 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 64 Proline residue: I 42 - end of helix Processing helix chain 'I' and resid 73 through 89 Processing helix chain 'I' and resid 90 through 100 removed outlier: 3.534A pdb=" N TRP I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 139 removed outlier: 3.928A pdb=" N VAL I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 155 through 167 removed outlier: 4.746A pdb=" N ILE I 162 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Proline residue: I 163 - end of helix Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'I' and resid 192 through 227 removed outlier: 3.742A pdb=" N VAL I 196 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU I 210 " --> pdb=" O VAL I 206 " (cutoff:3.500A) Proline residue: I 211 - end of helix removed outlier: 3.748A pdb=" N SER I 227 " --> pdb=" O ILE I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 234 No H-bonds generated for 'chain 'I' and resid 232 through 234' Processing helix chain 'I' and resid 235 through 266 removed outlier: 4.565A pdb=" N THR I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) Proline residue: I 254 - end of helix Processing helix chain 'I' and resid 273 through 290 Processing helix chain 'I' and resid 291 through 295 removed outlier: 3.643A pdb=" N HIS I 294 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 304 removed outlier: 3.537A pdb=" N LEU I 301 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR I 302 " --> pdb=" O ASN I 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 64 Proline residue: E 42 - end of helix Processing helix chain 'E' and resid 72 through 89 removed outlier: 4.346A pdb=" N TYR E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.507A pdb=" N TRP E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 139 removed outlier: 3.926A pdb=" N VAL E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 155 through 167 removed outlier: 4.642A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Proline residue: E 163 - end of helix Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 192 through 226 removed outlier: 3.839A pdb=" N VAL E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 210 " --> pdb=" O VAL E 206 " (cutoff:3.500A) Proline residue: E 211 - end of helix Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 232 through 234 No H-bonds generated for 'chain 'E' and resid 232 through 234' Processing helix chain 'E' and resid 235 through 266 removed outlier: 4.511A pdb=" N THR E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) Proline residue: E 254 - end of helix Processing helix chain 'E' and resid 275 through 290 removed outlier: 3.747A pdb=" N THR E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 295 removed outlier: 3.613A pdb=" N HIS E 294 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 304 removed outlier: 3.511A pdb=" N LEU E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 64 Proline residue: K 42 - end of helix Processing helix chain 'K' and resid 73 through 100 removed outlier: 3.801A pdb=" N THR K 90 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Proline residue: K 92 - end of helix Processing helix chain 'K' and resid 106 through 139 removed outlier: 3.990A pdb=" N VAL K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 154 Processing helix chain 'K' and resid 154 through 161 removed outlier: 4.184A pdb=" N VAL K 158 " --> pdb=" O LYS K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 166 Processing helix chain 'K' and resid 168 through 174 Processing helix chain 'K' and resid 192 through 227 removed outlier: 3.742A pdb=" N VAL K 196 " --> pdb=" O ASN K 192 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU K 210 " --> pdb=" O VAL K 206 " (cutoff:3.500A) Proline residue: K 211 - end of helix removed outlier: 3.659A pdb=" N SER K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 266 removed outlier: 3.668A pdb=" N LEU K 238 " --> pdb=" O LYS K 234 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR K 240 " --> pdb=" O LYS K 236 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) Proline residue: K 254 - end of helix Processing helix chain 'K' and resid 274 through 290 Processing helix chain 'K' and resid 291 through 295 removed outlier: 3.602A pdb=" N HIS K 294 " --> pdb=" O ALA K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 304 removed outlier: 3.578A pdb=" N TYR K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 64 Proline residue: L 42 - end of helix Processing helix chain 'L' and resid 73 through 89 Processing helix chain 'L' and resid 90 through 100 removed outlier: 3.529A pdb=" N TRP L 94 " --> pdb=" O THR L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 139 removed outlier: 4.018A pdb=" N VAL L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 154 Processing helix chain 'L' and resid 154 through 167 removed outlier: 4.492A pdb=" N VAL L 158 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE L 162 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Proline residue: L 163 - end of helix Processing helix chain 'L' and resid 168 through 174 Processing helix chain 'L' and resid 192 through 227 removed outlier: 3.782A pdb=" N VAL L 196 " --> pdb=" O ASN L 192 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU L 210 " --> pdb=" O VAL L 206 " (cutoff:3.500A) Proline residue: L 211 - end of helix removed outlier: 3.552A pdb=" N SER L 227 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 266 removed outlier: 4.408A pdb=" N THR L 240 " --> pdb=" O LYS L 236 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) Proline residue: L 254 - end of helix Processing helix chain 'L' and resid 273 through 290 Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.692A pdb=" N HIS L 294 " --> pdb=" O ALA L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 304 removed outlier: 3.538A pdb=" N LEU L 301 " --> pdb=" O LEU L 297 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR L 302 " --> pdb=" O ASN L 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 64 Processing helix chain 'M' and resid 55 through 64 Processing helix chain 'J' and resid 55 through 64 Processing helix chain 'F' and resid 55 through 64 Processing helix chain 'G' and resid 55 through 64 Processing helix chain 'H' and resid 55 through 63 Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.564A pdb=" N ASP A 187 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 48 through 51 removed outlier: 4.628A pdb=" N ILE N 38 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL N 39 " --> pdb=" O LEU N 26 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU N 26 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG N 41 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG M 41 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU M 26 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL M 39 " --> pdb=" O LEU M 26 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE M 38 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG M 47 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 47 through 51 removed outlier: 3.700A pdb=" N ARG O 47 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE O 38 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL O 39 " --> pdb=" O LEU O 26 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU O 26 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG O 41 " --> pdb=" O LYS O 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 26 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS F 25 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE F 38 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AA6, first strand: chain 'D' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'I' and resid 175 through 177 Processing sheet with id=AA8, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AA9, first strand: chain 'K' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'L' and resid 175 through 177 Processing sheet with id=AB2, first strand: chain 'P' and resid 47 through 51 removed outlier: 3.686A pdb=" N ARG P 47 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE P 38 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL P 39 " --> pdb=" O LEU P 26 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU P 26 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG P 41 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU G 26 " --> pdb=" O ILE P 28 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG G 41 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU G 26 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL G 39 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE G 28 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN G 37 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE G 38 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 47 through 51 removed outlier: 3.658A pdb=" N ARG J 47 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J 49 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE J 38 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL J 39 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU J 26 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG J 41 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS H 25 " --> pdb=" O ARG H 41 " (cutoff:3.500A) 1329 hydrogen bonds defined for protein. 3951 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: 3.02 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6557 1.36 - 1.49: 5759 1.49 - 1.62: 9215 1.62 - 1.75: 1 1.75 - 1.88: 151 Bond restraints: 21683 Sorted by residual: bond pdb=" N ASN E 278 " pdb=" CA ASN E 278 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.60e+00 bond pdb=" N VAL E 280 " pdb=" CA VAL E 280 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.87e+00 bond pdb=" CB CYS P 9 " pdb=" SG CYS P 9 " ideal model delta sigma weight residual 1.808 1.725 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB PRO A 27 " pdb=" CG PRO A 27 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.90e+00 bond pdb=" N ILE E 284 " pdb=" CA ILE E 284 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.14e-02 7.69e+03 5.68e+00 ... (remaining 21678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 29126 3.58 - 7.17: 362 7.17 - 10.75: 80 10.75 - 14.34: 13 14.34 - 17.92: 5 Bond angle restraints: 29586 Sorted by residual: angle pdb=" N PHE E 276 " pdb=" CA PHE E 276 " pdb=" C PHE E 276 " ideal model delta sigma weight residual 111.36 104.79 6.57 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N ILE C 39 " pdb=" CA ILE C 39 " pdb=" C ILE C 39 " ideal model delta sigma weight residual 112.96 107.13 5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" N ILE B 39 " pdb=" CA ILE B 39 " pdb=" C ILE B 39 " ideal model delta sigma weight residual 112.96 107.34 5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" CB MET I 205 " pdb=" CG MET I 205 " pdb=" SD MET I 205 " ideal model delta sigma weight residual 112.70 128.61 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" CB MET I 72 " pdb=" CG MET I 72 " pdb=" SD MET I 72 " ideal model delta sigma weight residual 112.70 128.29 -15.59 3.00e+00 1.11e-01 2.70e+01 ... (remaining 29581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 10666 15.55 - 31.11: 1505 31.11 - 46.66: 439 46.66 - 62.21: 127 62.21 - 77.77: 12 Dihedral angle restraints: 12749 sinusoidal: 4519 harmonic: 8230 Sorted by residual: dihedral pdb=" CB CYS O 9 " pdb=" SG CYS O 9 " pdb=" SG CYS O 11 " pdb=" CB CYS O 11 " ideal model delta sinusoidal sigma weight residual -86.00 -152.96 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS N 9 " pdb=" SG CYS N 9 " pdb=" SG CYS N 11 " pdb=" CB CYS N 11 " ideal model delta sinusoidal sigma weight residual -86.00 -146.16 60.16 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA CYS P 9 " pdb=" C CYS P 9 " pdb=" N PRO P 10 " pdb=" CA PRO P 10 " ideal model delta harmonic sigma weight residual 180.00 145.64 34.36 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 12746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2849 0.063 - 0.127: 595 0.127 - 0.190: 63 0.190 - 0.253: 12 0.253 - 0.317: 8 Chirality restraints: 3527 Sorted by residual: chirality pdb=" CB VAL E 155 " pdb=" CA VAL E 155 " pdb=" CG1 VAL E 155 " pdb=" CG2 VAL E 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VAL C 155 " pdb=" CA VAL C 155 " pdb=" CG1 VAL C 155 " pdb=" CG2 VAL C 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL I 155 " pdb=" CA VAL I 155 " pdb=" CG1 VAL I 155 " pdb=" CG2 VAL I 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3524 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 26 " -0.053 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 27 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 277 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" CD GLU C 277 " -0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU C 277 " 0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU C 277 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS G 9 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO G 10 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 10 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 10 " 0.038 5.00e-02 4.00e+02 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5817 2.81 - 3.33: 19784 3.33 - 3.86: 35643 3.86 - 4.38: 37206 4.38 - 4.90: 66002 Nonbonded interactions: 164452 Sorted by model distance: nonbonded pdb=" OH TYR M 7 " pdb=" O PRO M 32 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 117 " pdb=" OD2 ASP A 171 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR P 7 " pdb=" O ASN P 33 " model vdw 2.311 3.040 nonbonded pdb=" O ALA K 237 " pdb=" OG1 THR K 241 " model vdw 2.312 3.040 nonbonded pdb=" OG SER K 71 " pdb=" OD1 ASP K 74 " model vdw 2.316 3.040 ... (remaining 164447 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 305) selection = (chain 'B' and resid 26 through 305) selection = (chain 'C' and resid 26 through 305) selection = (chain 'D' and resid 26 through 305) selection = (chain 'E' and resid 26 through 305) selection = (chain 'I' and resid 26 through 305) selection = (chain 'K' and resid 26 through 305) selection = (chain 'L' and resid 26 through 305) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 3.900 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.690 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.005 0.121 21700 Z= 0.247 Angle : 1.044 17.921 29620 Z= 0.538 Chirality : 0.053 0.317 3527 Planarity : 0.007 0.077 3632 Dihedral : 16.449 77.768 7340 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 0.57 % Allowed : 31.48 % Favored : 67.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.68 % 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: -2.06 (0.15), residues: 2736 helix: -0.77 (0.11), residues: 1785 sheet: -1.47 (0.48), residues: 104 loop : -2.42 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 12 TYR 0.020 0.001 TYR G 7 PHE 0.046 0.001 PHE K 29 TRP 0.009 0.001 TRP L 283 HIS 0.007 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00485 (21683) covalent geometry : angle 1.03990 (29586) SS BOND : bond 0.00633 ( 17) SS BOND : angle 2.98412 ( 34) hydrogen bonds : bond 0.13526 ( 1329) hydrogen bonds : angle 6.64989 ( 3951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8607 (mm-30) REVERT: C 153 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8552 (mp0) REVERT: C 181 ASP cc_start: 0.8240 (p0) cc_final: 0.7870 (p0) REVERT: I 277 GLU cc_start: 0.8967 (tt0) cc_final: 0.8602 (tm-30) REVERT: E 220 CYS cc_start: 0.8575 (t) cc_final: 0.8304 (t) REVERT: E 283 TRP cc_start: 0.8915 (t-100) cc_final: 0.8608 (t-100) REVERT: P 9 CYS cc_start: 0.6849 (m) cc_final: 0.6597 (p) outliers start: 12 outliers final: 3 residues processed: 234 average time/residue: 0.1351 time to fit residues: 50.5522 Evaluate side-chains 211 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain J residue 9 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN C 56 ASN L 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081394 restraints weight = 53129.978| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.80 r_work: 0.3102 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21700 Z= 0.110 Angle : 0.584 12.047 29620 Z= 0.294 Chirality : 0.041 0.152 3527 Planarity : 0.004 0.052 3632 Dihedral : 4.877 56.019 2964 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 2.97 % Allowed : 27.47 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -0.24 (0.17), residues: 2736 helix: 0.88 (0.12), residues: 1791 sheet: -1.39 (0.47), residues: 104 loop : -2.28 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 183 TYR 0.012 0.001 TYR P 7 PHE 0.019 0.001 PHE K 29 TRP 0.009 0.001 TRP C 283 HIS 0.005 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00216 (21683) covalent geometry : angle 0.58334 (29586) SS BOND : bond 0.00711 ( 17) SS BOND : angle 1.22262 ( 34) hydrogen bonds : bond 0.03979 ( 1329) hydrogen bonds : angle 4.90896 ( 3951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8339 (mm-30) REVERT: N 7 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8628 (p90) REVERT: O 9 CYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6784 (p) REVERT: C 181 ASP cc_start: 0.8181 (p0) cc_final: 0.7913 (p0) REVERT: D 277 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8267 (tm-30) REVERT: I 205 MET cc_start: 0.8468 (tpp) cc_final: 0.8194 (tpp) REVERT: I 277 GLU cc_start: 0.8899 (tt0) cc_final: 0.8501 (tm-30) REVERT: E 26 GLU cc_start: 0.8800 (mp0) cc_final: 0.7921 (tm-30) REVERT: E 201 PHE cc_start: 0.8379 (m-10) cc_final: 0.8149 (m-10) REVERT: E 283 TRP cc_start: 0.8811 (t-100) cc_final: 0.8427 (t-100) REVERT: E 288 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9261 (tm-30) REVERT: K 84 ASP cc_start: 0.8932 (m-30) cc_final: 0.8472 (t0) REVERT: L 72 MET cc_start: 0.8641 (tpp) cc_final: 0.8410 (tpp) REVERT: L 183 ARG cc_start: 0.7176 (tpm170) cc_final: 0.6932 (tpm170) REVERT: L 205 MET cc_start: 0.8290 (tpp) cc_final: 0.8011 (tpt) REVERT: P 9 CYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6590 (p) outliers start: 63 outliers final: 32 residues processed: 262 average time/residue: 0.1253 time to fit residues: 53.6602 Evaluate side-chains 233 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 7 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain J residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 171 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 267 optimal weight: 0.0010 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 172 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 overall best weight: 0.8324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN A 281 HIS K 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079956 restraints weight = 54476.632| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.81 r_work: 0.3086 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21700 Z= 0.109 Angle : 0.558 10.561 29620 Z= 0.280 Chirality : 0.041 0.145 3527 Planarity : 0.004 0.049 3632 Dihedral : 4.601 53.180 2962 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 3.02 % Allowed : 27.89 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.48 (0.17), residues: 2736 helix: 1.55 (0.13), residues: 1791 sheet: -1.46 (0.46), residues: 104 loop : -2.23 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 12 TYR 0.011 0.001 TYR G 7 PHE 0.015 0.001 PHE K 29 TRP 0.008 0.001 TRP C 283 HIS 0.004 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00228 (21683) covalent geometry : angle 0.55652 (29586) SS BOND : bond 0.00294 ( 17) SS BOND : angle 1.21420 ( 34) hydrogen bonds : bond 0.03716 ( 1329) hydrogen bonds : angle 4.53744 ( 3951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 211 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 84 ASP cc_start: 0.8951 (m-30) cc_final: 0.8645 (t0) REVERT: A 182 ASP cc_start: 0.8879 (p0) cc_final: 0.8664 (p0) REVERT: A 218 CYS cc_start: 0.9100 (m) cc_final: 0.8885 (m) REVERT: A 277 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8370 (tm-30) REVERT: N 7 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8700 (p90) REVERT: O 9 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6978 (p) REVERT: D 26 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 277 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8126 (tm-30) REVERT: I 29 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8073 (t80) REVERT: I 205 MET cc_start: 0.8335 (tpp) cc_final: 0.7965 (tpt) REVERT: I 277 GLU cc_start: 0.8909 (tt0) cc_final: 0.8510 (tm-30) REVERT: E 26 GLU cc_start: 0.8822 (mp0) cc_final: 0.7567 (tm-30) REVERT: E 29 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: E 183 ARG cc_start: 0.7256 (tpm170) cc_final: 0.7054 (tpm170) REVERT: E 201 PHE cc_start: 0.8416 (m-10) cc_final: 0.8148 (m-10) REVERT: E 283 TRP cc_start: 0.8866 (t-100) cc_final: 0.8621 (t-100) REVERT: E 288 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9218 (tm-30) REVERT: K 72 MET cc_start: 0.8821 (tpp) cc_final: 0.8502 (tpp) REVERT: K 84 ASP cc_start: 0.9062 (m-30) cc_final: 0.8530 (t0) REVERT: K 205 MET cc_start: 0.8448 (tpp) cc_final: 0.8118 (tpt) REVERT: K 251 CYS cc_start: 0.9208 (m) cc_final: 0.8951 (m) REVERT: L 72 MET cc_start: 0.8814 (tpp) cc_final: 0.8563 (tpp) REVERT: L 183 ARG cc_start: 0.7166 (tpm170) cc_final: 0.6854 (tpm170) REVERT: L 205 MET cc_start: 0.8272 (tpp) cc_final: 0.7996 (tpt) REVERT: L 277 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8596 (tm-30) REVERT: P 9 CYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6576 (p) REVERT: M 9 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6982 (p) REVERT: J 9 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6789 (p) outliers start: 64 outliers final: 34 residues processed: 253 average time/residue: 0.1278 time to fit residues: 52.0966 Evaluate side-chains 239 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 7 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain J residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 199 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 263 optimal weight: 40.0000 chunk 223 optimal weight: 0.5980 chunk 244 optimal weight: 40.0000 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 ASN ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075797 restraints weight = 55253.621| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.80 r_work: 0.2984 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21700 Z= 0.174 Angle : 0.588 11.408 29620 Z= 0.300 Chirality : 0.043 0.161 3527 Planarity : 0.004 0.050 3632 Dihedral : 4.573 51.374 2962 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 3.49 % Allowed : 27.84 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.79 (0.18), residues: 2736 helix: 1.91 (0.13), residues: 1792 sheet: -2.37 (0.36), residues: 144 loop : -2.23 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 183 TYR 0.013 0.001 TYR A 219 PHE 0.012 0.001 PHE K 29 TRP 0.011 0.001 TRP B 283 HIS 0.003 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00401 (21683) covalent geometry : angle 0.58693 (29586) SS BOND : bond 0.00354 ( 17) SS BOND : angle 1.20735 ( 34) hydrogen bonds : bond 0.04215 ( 1329) hydrogen bonds : angle 4.47076 ( 3951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 200 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.8849 (m-30) cc_final: 0.8194 (t0) REVERT: A 84 ASP cc_start: 0.9077 (m-30) cc_final: 0.8647 (t0) REVERT: A 183 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7616 (mmm160) REVERT: A 277 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8408 (tm-30) REVERT: O 9 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7118 (p) REVERT: C 84 ASP cc_start: 0.8855 (m-30) cc_final: 0.8180 (t0) REVERT: D 26 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7716 (tm-30) REVERT: D 153 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8863 (mm-30) REVERT: D 277 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8339 (tm-30) REVERT: I 29 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8026 (t80) REVERT: I 72 MET cc_start: 0.8942 (tpp) cc_final: 0.8733 (tpp) REVERT: I 205 MET cc_start: 0.8332 (tpp) cc_final: 0.7917 (tpt) REVERT: I 277 GLU cc_start: 0.8979 (tt0) cc_final: 0.8565 (tm-30) REVERT: E 26 GLU cc_start: 0.8886 (mp0) cc_final: 0.7936 (tm-30) REVERT: E 29 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7912 (t80) REVERT: E 183 ARG cc_start: 0.7471 (tpm170) cc_final: 0.7231 (tpm170) REVERT: E 205 MET cc_start: 0.8345 (tpp) cc_final: 0.8122 (tpt) REVERT: E 275 GLU cc_start: 0.9143 (tp30) cc_final: 0.8914 (tp30) REVERT: E 283 TRP cc_start: 0.8996 (t-100) cc_final: 0.8637 (t-100) REVERT: E 288 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9227 (tm-30) REVERT: K 72 MET cc_start: 0.9026 (tpp) cc_final: 0.8684 (tpp) REVERT: K 84 ASP cc_start: 0.9261 (m-30) cc_final: 0.8818 (t0) REVERT: K 205 MET cc_start: 0.8409 (tpp) cc_final: 0.8196 (tpp) REVERT: K 229 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8310 (t) REVERT: K 251 CYS cc_start: 0.9244 (m) cc_final: 0.8929 (m) REVERT: L 72 MET cc_start: 0.9024 (tpp) cc_final: 0.8677 (tpp) REVERT: L 183 ARG cc_start: 0.7122 (tpm170) cc_final: 0.6723 (tpm170) REVERT: L 205 MET cc_start: 0.8292 (tpp) cc_final: 0.7926 (tpt) REVERT: L 277 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8646 (tm-30) REVERT: M 9 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6806 (p) REVERT: J 9 CYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6953 (p) outliers start: 74 outliers final: 52 residues processed: 248 average time/residue: 0.1369 time to fit residues: 54.8881 Evaluate side-chains 240 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 229 SER Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain J residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 266 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 92 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 152 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 119 ASN K 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077826 restraints weight = 54287.560| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.76 r_work: 0.3034 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21700 Z= 0.113 Angle : 0.550 10.663 29620 Z= 0.278 Chirality : 0.041 0.150 3527 Planarity : 0.004 0.049 3632 Dihedral : 4.502 45.718 2962 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 3.73 % Allowed : 27.80 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.93 (0.18), residues: 2736 helix: 2.02 (0.13), residues: 1792 sheet: -2.29 (0.36), residues: 144 loop : -2.18 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 12 TYR 0.011 0.001 TYR G 7 PHE 0.012 0.001 PHE K 29 TRP 0.009 0.001 TRP B 283 HIS 0.003 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00240 (21683) covalent geometry : angle 0.54888 (29586) SS BOND : bond 0.00606 ( 17) SS BOND : angle 1.02645 ( 34) hydrogen bonds : bond 0.03786 ( 1329) hydrogen bonds : angle 4.32712 ( 3951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 205 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.8746 (m-30) cc_final: 0.8126 (t0) REVERT: B 268 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8450 (mm-30) REVERT: A 84 ASP cc_start: 0.8982 (m-30) cc_final: 0.8538 (t0) REVERT: A 218 CYS cc_start: 0.9144 (m) cc_final: 0.8793 (m) REVERT: A 277 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8343 (tm-30) REVERT: O 9 CYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7120 (p) REVERT: C 84 ASP cc_start: 0.8770 (m-30) cc_final: 0.8137 (t0) REVERT: C 179 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8320 (mm-30) REVERT: C 281 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8096 (t70) REVERT: D 26 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 84 ASP cc_start: 0.8654 (m-30) cc_final: 0.8172 (t0) REVERT: D 153 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8822 (mm-30) REVERT: I 29 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7989 (t80) REVERT: I 72 MET cc_start: 0.9030 (tpp) cc_final: 0.8739 (tpp) REVERT: I 205 MET cc_start: 0.8254 (tpp) cc_final: 0.7813 (tpt) REVERT: I 220 CYS cc_start: 0.8805 (t) cc_final: 0.8572 (t) REVERT: I 277 GLU cc_start: 0.8936 (tt0) cc_final: 0.8510 (tm-30) REVERT: E 26 GLU cc_start: 0.8811 (mp0) cc_final: 0.8020 (tm-30) REVERT: E 29 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7846 (t80) REVERT: E 183 ARG cc_start: 0.7471 (tpm170) cc_final: 0.7181 (tpm170) REVERT: E 201 PHE cc_start: 0.8575 (m-80) cc_final: 0.8288 (m-10) REVERT: E 205 MET cc_start: 0.8296 (tpp) cc_final: 0.7999 (tpt) REVERT: E 275 GLU cc_start: 0.9181 (tp30) cc_final: 0.8961 (tp30) REVERT: E 283 TRP cc_start: 0.8971 (t-100) cc_final: 0.8584 (t-100) REVERT: E 288 GLU cc_start: 0.9554 (tm-30) cc_final: 0.9178 (tm-30) REVERT: K 72 MET cc_start: 0.8999 (tpp) cc_final: 0.8634 (tpp) REVERT: K 84 ASP cc_start: 0.9186 (m-30) cc_final: 0.8737 (t0) REVERT: K 187 ASP cc_start: 0.8055 (t0) cc_final: 0.7710 (t0) REVERT: K 205 MET cc_start: 0.8379 (tpp) cc_final: 0.8050 (tpt) REVERT: K 229 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8317 (t) REVERT: L 72 MET cc_start: 0.9069 (tpp) cc_final: 0.8707 (tpp) REVERT: L 183 ARG cc_start: 0.7132 (tpm170) cc_final: 0.6752 (tpm170) REVERT: L 205 MET cc_start: 0.8249 (tpp) cc_final: 0.8039 (tpp) REVERT: L 277 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8619 (tm-30) REVERT: P 9 CYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6553 (p) REVERT: M 9 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6691 (p) outliers start: 79 outliers final: 50 residues processed: 263 average time/residue: 0.1197 time to fit residues: 51.4345 Evaluate side-chains 244 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 229 SER Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.103704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078630 restraints weight = 53898.147| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.79 r_work: 0.3033 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21700 Z= 0.116 Angle : 0.552 11.149 29620 Z= 0.279 Chirality : 0.041 0.148 3527 Planarity : 0.004 0.048 3632 Dihedral : 4.349 31.438 2961 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 3.87 % Allowed : 27.80 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 1.03 (0.18), residues: 2736 helix: 2.10 (0.13), residues: 1792 sheet: -2.30 (0.35), residues: 154 loop : -2.14 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 12 TYR 0.011 0.001 TYR G 7 PHE 0.012 0.001 PHE K 29 TRP 0.008 0.001 TRP B 283 HIS 0.002 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00254 (21683) covalent geometry : angle 0.55064 (29586) SS BOND : bond 0.00383 ( 17) SS BOND : angle 1.12345 ( 34) hydrogen bonds : bond 0.03744 ( 1329) hydrogen bonds : angle 4.26412 ( 3951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 198 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 84 ASP cc_start: 0.9002 (m-30) cc_final: 0.8514 (t0) REVERT: A 183 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7357 (mmm160) REVERT: A 218 CYS cc_start: 0.9059 (m) cc_final: 0.8736 (m) REVERT: A 277 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8332 (tm-30) REVERT: O 9 CYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7150 (p) REVERT: C 74 ASP cc_start: 0.9016 (m-30) cc_final: 0.8694 (m-30) REVERT: C 281 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8193 (t70) REVERT: D 26 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 84 ASP cc_start: 0.8703 (m-30) cc_final: 0.8183 (t0) REVERT: D 153 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8811 (mm-30) REVERT: D 277 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7994 (tm-30) REVERT: I 29 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8059 (t80) REVERT: I 72 MET cc_start: 0.9076 (tpp) cc_final: 0.8631 (tpp) REVERT: I 187 ASP cc_start: 0.7917 (t70) cc_final: 0.7566 (t0) REVERT: I 205 MET cc_start: 0.8214 (tpp) cc_final: 0.7919 (tpp) REVERT: I 220 CYS cc_start: 0.8865 (t) cc_final: 0.8640 (t) REVERT: I 277 GLU cc_start: 0.8916 (tt0) cc_final: 0.8500 (tm-30) REVERT: E 26 GLU cc_start: 0.8815 (mp0) cc_final: 0.8107 (tm-30) REVERT: E 29 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7849 (t80) REVERT: E 31 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 183 ARG cc_start: 0.7491 (tpm170) cc_final: 0.7171 (tpm170) REVERT: E 201 PHE cc_start: 0.8581 (m-80) cc_final: 0.8286 (m-10) REVERT: E 283 TRP cc_start: 0.8971 (t-100) cc_final: 0.8659 (t-100) REVERT: E 288 GLU cc_start: 0.9574 (tm-30) cc_final: 0.9171 (tm-30) REVERT: K 72 MET cc_start: 0.9041 (tpp) cc_final: 0.8563 (tpp) REVERT: K 84 ASP cc_start: 0.9216 (m-30) cc_final: 0.8642 (t0) REVERT: K 187 ASP cc_start: 0.8053 (t0) cc_final: 0.7708 (t0) REVERT: K 205 MET cc_start: 0.8372 (tpp) cc_final: 0.8030 (tpt) REVERT: K 229 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8325 (t) REVERT: L 72 MET cc_start: 0.9119 (tpp) cc_final: 0.8725 (tpp) REVERT: L 183 ARG cc_start: 0.7156 (tpm170) cc_final: 0.6739 (tpm170) REVERT: L 205 MET cc_start: 0.8227 (tpp) cc_final: 0.8011 (tpp) REVERT: L 277 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8608 (tm-30) REVERT: P 9 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6566 (p) REVERT: M 9 CYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6613 (p) outliers start: 82 outliers final: 64 residues processed: 256 average time/residue: 0.1201 time to fit residues: 50.8046 Evaluate side-chains 260 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 229 SER Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain J residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 198 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075628 restraints weight = 54782.648| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.75 r_work: 0.2984 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21700 Z= 0.169 Angle : 0.589 10.755 29620 Z= 0.302 Chirality : 0.042 0.152 3527 Planarity : 0.004 0.050 3632 Dihedral : 4.389 31.501 2961 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 3.92 % Allowed : 27.84 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 1.08 (0.18), residues: 2736 helix: 2.13 (0.13), residues: 1792 sheet: -2.26 (0.37), residues: 144 loop : -2.13 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 12 TYR 0.012 0.001 TYR A 103 PHE 0.011 0.001 PHE D 199 TRP 0.012 0.001 TRP D 283 HIS 0.002 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00394 (21683) covalent geometry : angle 0.58766 (29586) SS BOND : bond 0.00404 ( 17) SS BOND : angle 1.19188 ( 34) hydrogen bonds : bond 0.04095 ( 1329) hydrogen bonds : angle 4.34412 ( 3951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.8807 (m-30) cc_final: 0.8167 (t0) REVERT: B 268 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8517 (mm-30) REVERT: A 153 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8934 (mm-30) REVERT: A 182 ASP cc_start: 0.8884 (p0) cc_final: 0.8631 (p0) REVERT: A 218 CYS cc_start: 0.9168 (m) cc_final: 0.8882 (m) REVERT: A 277 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8353 (tm-30) REVERT: O 9 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7119 (p) REVERT: C 30 ARG cc_start: 0.8213 (tpt-90) cc_final: 0.7722 (mmt180) REVERT: C 84 ASP cc_start: 0.8836 (m-30) cc_final: 0.8204 (t0) REVERT: C 179 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 26 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7572 (tm-30) REVERT: D 153 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8734 (mm-30) REVERT: D 183 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7506 (mmm-85) REVERT: D 277 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7997 (tm-30) REVERT: I 29 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8070 (t80) REVERT: I 72 MET cc_start: 0.9154 (tpp) cc_final: 0.8590 (tpp) REVERT: I 187 ASP cc_start: 0.8033 (t70) cc_final: 0.7669 (t0) REVERT: I 205 MET cc_start: 0.8277 (tpp) cc_final: 0.7976 (tpp) REVERT: I 220 CYS cc_start: 0.8928 (t) cc_final: 0.8702 (t) REVERT: I 277 GLU cc_start: 0.8962 (tt0) cc_final: 0.8552 (tm-30) REVERT: E 26 GLU cc_start: 0.8833 (mp0) cc_final: 0.8118 (tm-30) REVERT: E 29 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7846 (t80) REVERT: E 183 ARG cc_start: 0.7553 (tpm170) cc_final: 0.7322 (tpm170) REVERT: E 268 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8237 (mp0) REVERT: E 275 GLU cc_start: 0.9125 (tp30) cc_final: 0.8900 (tp30) REVERT: E 283 TRP cc_start: 0.8954 (t-100) cc_final: 0.8508 (t-100) REVERT: E 288 GLU cc_start: 0.9586 (tm-30) cc_final: 0.9304 (tm-30) REVERT: K 72 MET cc_start: 0.9093 (tpp) cc_final: 0.8588 (tpp) REVERT: K 187 ASP cc_start: 0.8075 (t0) cc_final: 0.7721 (t0) REVERT: K 205 MET cc_start: 0.8389 (tpp) cc_final: 0.8034 (tpt) REVERT: K 251 CYS cc_start: 0.9227 (m) cc_final: 0.8998 (m) REVERT: K 288 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9251 (tm-30) REVERT: L 72 MET cc_start: 0.9180 (tpp) cc_final: 0.8728 (tpp) REVERT: L 183 ARG cc_start: 0.7208 (tpm170) cc_final: 0.6761 (tpm170) REVERT: L 277 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8634 (tm-30) REVERT: P 9 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6523 (p) REVERT: M 9 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6709 (p) outliers start: 83 outliers final: 63 residues processed: 251 average time/residue: 0.1249 time to fit residues: 51.3309 Evaluate side-chains 254 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 186 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 268 optimal weight: 50.0000 chunk 140 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 92 optimal weight: 0.0000 chunk 222 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076988 restraints weight = 54267.035| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.84 r_work: 0.3019 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21700 Z= 0.118 Angle : 0.569 10.876 29620 Z= 0.289 Chirality : 0.041 0.154 3527 Planarity : 0.004 0.048 3632 Dihedral : 4.351 31.482 2961 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 3.82 % Allowed : 27.94 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 1.13 (0.18), residues: 2736 helix: 2.16 (0.13), residues: 1792 sheet: -2.25 (0.35), residues: 154 loop : -2.06 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 12 TYR 0.011 0.001 TYR G 7 PHE 0.011 0.001 PHE K 29 TRP 0.009 0.001 TRP C 283 HIS 0.002 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00257 (21683) covalent geometry : angle 0.56772 (29586) SS BOND : bond 0.00414 ( 17) SS BOND : angle 1.34800 ( 34) hydrogen bonds : bond 0.03796 ( 1329) hydrogen bonds : angle 4.24353 ( 3951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 191 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.8770 (m-30) cc_final: 0.8111 (t0) REVERT: B 268 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8459 (mm-30) REVERT: A 84 ASP cc_start: 0.8987 (m-30) cc_final: 0.8516 (t0) REVERT: A 182 ASP cc_start: 0.8911 (p0) cc_final: 0.8683 (p0) REVERT: A 218 CYS cc_start: 0.9082 (m) cc_final: 0.8771 (m) REVERT: A 277 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8323 (tm-30) REVERT: O 9 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7099 (p) REVERT: C 74 ASP cc_start: 0.8821 (m-30) cc_final: 0.8554 (m-30) REVERT: C 84 ASP cc_start: 0.8771 (m-30) cc_final: 0.8118 (t0) REVERT: C 281 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8096 (t70) REVERT: D 26 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 84 ASP cc_start: 0.8765 (m-30) cc_final: 0.8147 (t0) REVERT: D 153 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8706 (mm-30) REVERT: D 277 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8019 (tm-30) REVERT: I 29 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8051 (t80) REVERT: I 72 MET cc_start: 0.9140 (tpp) cc_final: 0.8531 (tpp) REVERT: I 187 ASP cc_start: 0.7969 (t70) cc_final: 0.7627 (t0) REVERT: I 205 MET cc_start: 0.8235 (tpp) cc_final: 0.7936 (tpp) REVERT: I 220 CYS cc_start: 0.8922 (t) cc_final: 0.8697 (t) REVERT: I 277 GLU cc_start: 0.8923 (tt0) cc_final: 0.8508 (tm-30) REVERT: E 26 GLU cc_start: 0.8789 (mp0) cc_final: 0.8129 (tm-30) REVERT: E 29 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7827 (t80) REVERT: E 31 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 183 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7254 (tpm170) REVERT: E 201 PHE cc_start: 0.8579 (m-80) cc_final: 0.8319 (m-10) REVERT: E 268 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8177 (mp0) REVERT: E 283 TRP cc_start: 0.8881 (t-100) cc_final: 0.8482 (t-100) REVERT: K 72 MET cc_start: 0.9093 (tpp) cc_final: 0.8550 (tpp) REVERT: K 84 ASP cc_start: 0.9044 (m-30) cc_final: 0.8690 (t0) REVERT: K 187 ASP cc_start: 0.8038 (t0) cc_final: 0.7706 (t0) REVERT: K 205 MET cc_start: 0.8357 (tpp) cc_final: 0.8014 (tpt) REVERT: K 251 CYS cc_start: 0.9216 (m) cc_final: 0.8977 (m) REVERT: K 302 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: L 72 MET cc_start: 0.9176 (tpp) cc_final: 0.8707 (tpp) REVERT: L 183 ARG cc_start: 0.7171 (tpm170) cc_final: 0.6756 (tpm170) REVERT: L 205 MET cc_start: 0.8389 (tpp) cc_final: 0.8123 (tpt) REVERT: L 277 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8631 (tm-30) REVERT: P 9 CYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6585 (p) REVERT: M 9 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6719 (p) outliers start: 81 outliers final: 63 residues processed: 249 average time/residue: 0.1234 time to fit residues: 50.3923 Evaluate side-chains 254 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 302 TYR Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 18 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073810 restraints weight = 55548.403| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.94 r_work: 0.2933 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21700 Z= 0.153 Angle : 0.595 10.728 29620 Z= 0.303 Chirality : 0.042 0.163 3527 Planarity : 0.004 0.046 3632 Dihedral : 4.348 31.490 2961 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 3.87 % Allowed : 27.84 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 1.17 (0.18), residues: 2736 helix: 2.19 (0.13), residues: 1792 sheet: -2.16 (0.37), residues: 144 loop : -2.08 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 12 TYR 0.011 0.001 TYR A 103 PHE 0.011 0.001 PHE K 29 TRP 0.009 0.001 TRP B 283 HIS 0.002 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00353 (21683) covalent geometry : angle 0.59381 (29586) SS BOND : bond 0.00394 ( 17) SS BOND : angle 1.25937 ( 34) hydrogen bonds : bond 0.03968 ( 1329) hydrogen bonds : angle 4.27542 ( 3951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 189 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8524 (mm-30) REVERT: A 84 ASP cc_start: 0.9061 (m-30) cc_final: 0.8569 (t0) REVERT: A 153 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8972 (mm-30) REVERT: A 182 ASP cc_start: 0.8922 (p0) cc_final: 0.8666 (p0) REVERT: A 183 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7429 (mmm160) REVERT: A 218 CYS cc_start: 0.9172 (m) cc_final: 0.8844 (m) REVERT: A 277 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8390 (tm-30) REVERT: O 9 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7090 (p) REVERT: C 84 ASP cc_start: 0.8853 (m-30) cc_final: 0.8180 (t0) REVERT: C 179 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8158 (mm-30) REVERT: D 26 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7570 (tm-30) REVERT: D 84 ASP cc_start: 0.8802 (m-30) cc_final: 0.8142 (t0) REVERT: D 153 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8700 (mm-30) REVERT: D 183 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7738 (mmm-85) REVERT: D 277 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8071 (tm-30) REVERT: I 29 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8052 (t80) REVERT: I 72 MET cc_start: 0.9158 (tpp) cc_final: 0.8553 (tpp) REVERT: I 187 ASP cc_start: 0.8011 (t70) cc_final: 0.7658 (t0) REVERT: I 205 MET cc_start: 0.8250 (tpp) cc_final: 0.7951 (tpp) REVERT: I 220 CYS cc_start: 0.8924 (t) cc_final: 0.8708 (t) REVERT: I 277 GLU cc_start: 0.8935 (tt0) cc_final: 0.8521 (tm-30) REVERT: E 26 GLU cc_start: 0.8789 (mp0) cc_final: 0.8131 (tm-30) REVERT: E 29 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7843 (t80) REVERT: E 31 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 183 ARG cc_start: 0.7598 (tpm170) cc_final: 0.7361 (tpm170) REVERT: E 201 PHE cc_start: 0.8625 (m-80) cc_final: 0.8337 (m-10) REVERT: E 268 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8225 (mp0) REVERT: E 283 TRP cc_start: 0.8898 (t-100) cc_final: 0.8492 (t-100) REVERT: E 288 GLU cc_start: 0.9525 (tm-30) cc_final: 0.9298 (tm-30) REVERT: K 72 MET cc_start: 0.9117 (tpp) cc_final: 0.8546 (tpp) REVERT: K 84 ASP cc_start: 0.9147 (m-30) cc_final: 0.8739 (t0) REVERT: K 187 ASP cc_start: 0.8034 (t0) cc_final: 0.7698 (t0) REVERT: K 205 MET cc_start: 0.8372 (tpp) cc_final: 0.8014 (tpt) REVERT: K 251 CYS cc_start: 0.9221 (m) cc_final: 0.8975 (m) REVERT: L 72 MET cc_start: 0.9209 (tpp) cc_final: 0.8711 (tpp) REVERT: L 183 ARG cc_start: 0.7182 (tpm170) cc_final: 0.6743 (tpm170) REVERT: L 205 MET cc_start: 0.8400 (tpp) cc_final: 0.8132 (tpt) REVERT: L 277 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8667 (tm-30) REVERT: P 9 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6514 (p) REVERT: M 9 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6798 (p) outliers start: 82 outliers final: 68 residues processed: 252 average time/residue: 0.1246 time to fit residues: 51.5421 Evaluate side-chains 261 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 230 LYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 172 PHE Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain J residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 173 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 184 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.072278 restraints weight = 55165.983| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.87 r_work: 0.2885 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21700 Z= 0.240 Angle : 0.659 11.041 29620 Z= 0.340 Chirality : 0.044 0.161 3527 Planarity : 0.004 0.049 3632 Dihedral : 4.550 31.862 2961 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.78 % Allowed : 28.13 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 1.05 (0.18), residues: 2736 helix: 2.09 (0.13), residues: 1792 sheet: -2.31 (0.35), residues: 154 loop : -2.07 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 12 TYR 0.014 0.001 TYR A 103 PHE 0.013 0.001 PHE A 199 TRP 0.013 0.001 TRP B 283 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00561 (21683) covalent geometry : angle 0.65737 (29586) SS BOND : bond 0.00498 ( 17) SS BOND : angle 1.38577 ( 34) hydrogen bonds : bond 0.04586 ( 1329) hydrogen bonds : angle 4.53287 ( 3951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 185 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASP cc_start: 0.8882 (m-30) cc_final: 0.8253 (t0) REVERT: B 268 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 84 ASP cc_start: 0.9169 (m-30) cc_final: 0.8626 (t0) REVERT: A 153 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8927 (mm-30) REVERT: A 182 ASP cc_start: 0.8938 (p0) cc_final: 0.8707 (p0) REVERT: A 183 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7424 (mmm160) REVERT: A 277 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8425 (tm-30) REVERT: O 9 CYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6929 (p) REVERT: C 84 ASP cc_start: 0.8954 (m-30) cc_final: 0.8402 (t0) REVERT: D 26 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 84 ASP cc_start: 0.8925 (m-30) cc_final: 0.8284 (t0) REVERT: D 153 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 171 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: D 277 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8058 (tm-30) REVERT: I 29 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8001 (t80) REVERT: I 72 MET cc_start: 0.9189 (tpp) cc_final: 0.8566 (tpp) REVERT: I 187 ASP cc_start: 0.8017 (t70) cc_final: 0.7631 (t0) REVERT: I 205 MET cc_start: 0.8265 (tpp) cc_final: 0.8018 (tpp) REVERT: I 220 CYS cc_start: 0.8955 (t) cc_final: 0.8741 (t) REVERT: I 277 GLU cc_start: 0.8976 (tt0) cc_final: 0.8577 (tm-30) REVERT: E 26 GLU cc_start: 0.8806 (mp0) cc_final: 0.8067 (tm-30) REVERT: E 29 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7857 (t80) REVERT: E 31 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8018 (tm-30) REVERT: E 183 ARG cc_start: 0.7617 (tpm170) cc_final: 0.7321 (tpm170) REVERT: E 205 MET cc_start: 0.8474 (tpp) cc_final: 0.8212 (tpt) REVERT: E 268 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8419 (mp0) REVERT: E 283 TRP cc_start: 0.8893 (t-100) cc_final: 0.8615 (t-100) REVERT: K 72 MET cc_start: 0.9121 (tpp) cc_final: 0.8528 (tpp) REVERT: K 84 ASP cc_start: 0.9219 (m-30) cc_final: 0.8825 (t0) REVERT: K 187 ASP cc_start: 0.8042 (t0) cc_final: 0.7754 (t0) REVERT: K 220 CYS cc_start: 0.8922 (t) cc_final: 0.8692 (t) REVERT: K 251 CYS cc_start: 0.9208 (m) cc_final: 0.8962 (m) REVERT: L 72 MET cc_start: 0.9207 (tpp) cc_final: 0.8648 (tpp) REVERT: L 183 ARG cc_start: 0.7286 (tpm170) cc_final: 0.6959 (tpm170) REVERT: L 205 MET cc_start: 0.8377 (tpp) cc_final: 0.8086 (tpt) REVERT: M 9 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6749 (p) outliers start: 80 outliers final: 67 residues processed: 246 average time/residue: 0.1275 time to fit residues: 50.9088 Evaluate side-chains 250 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 9 CYS Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 186 CYS Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 186 CYS Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 265 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 186 CYS Chi-restraints excluded: chain L residue 265 ILE Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain M residue 9 CYS Chi-restraints excluded: chain G residue 7 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.098208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072532 restraints weight = 54913.472| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.87 r_work: 0.2889 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 21700 Z= 0.230 Angle : 0.797 59.198 29620 Z= 0.447 Chirality : 0.045 0.821 3527 Planarity : 0.004 0.068 3632 Dihedral : 4.632 43.676 2961 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 3.59 % Allowed : 28.69 % Favored : 67.72 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.04 % 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: 1.05 (0.18), residues: 2736 helix: 2.10 (0.13), residues: 1792 sheet: -2.31 (0.36), residues: 154 loop : -2.08 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 12 TYR 0.038 0.002 TYR L 184 PHE 0.013 0.001 PHE A 199 TRP 0.011 0.001 TRP B 283 HIS 0.004 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00495 (21683) covalent geometry : angle 0.79222 (29586) SS BOND : bond 0.00678 ( 17) SS BOND : angle 2.56962 ( 34) hydrogen bonds : bond 0.04565 ( 1329) hydrogen bonds : angle 4.53305 ( 3951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.37 seconds wall clock time: 64 minutes 24.24 seconds (3864.24 seconds total)