Starting phenix.real_space_refine on Fri Jul 3 09:46:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lr2_63313/07_2026/9lr2_63313.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 98 5.16 5 C 8525 2.51 5 N 2124 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13115 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1703 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2311 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2135 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 752 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'TYR:plan': 5, 'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 130 Chain: "C" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 894 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 246 Unusual residues: {'CLR': 7, 'PCF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "Q" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 246 Unusual residues: {'CLR': 7, 'PCF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.41, per 1000 atoms: 0.18 Number of scatterers: 13115 At special positions: 0 Unit cell: (114.39, 119.04, 160.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 2 15.00 O 2366 8.00 N 2124 7.00 C 8525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 102 " - pdb=" SG CYS Q 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.11 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: 0.77 Conformation dependent library (CDL) restraints added in 408.9 milliseconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 19 sheets defined 41.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.790A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.178A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.629A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.777A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'R' and resid 29 through 54 Processing helix chain 'R' and resid 64 through 77 removed outlier: 3.557A pdb=" N ILE R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.636A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 3.931A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 161 removed outlier: 3.552A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.756A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 removed outlier: 4.296A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 240 through 259 removed outlier: 3.574A pdb=" N VAL R 254 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 272 removed outlier: 3.572A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 298 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 removed outlier: 3.612A pdb=" N ARG R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 54 removed outlier: 3.515A pdb=" N PHE Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 80 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'Q' and resid 98 through 130 Processing helix chain 'Q' and resid 135 through 144 removed outlier: 3.915A pdb=" N ARG Q 139 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG Q 143 " --> pdb=" O ARG Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 161 removed outlier: 3.828A pdb=" N VAL Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU Q 153 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 172 through 176 removed outlier: 3.721A pdb=" N THR Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 210 removed outlier: 3.686A pdb=" N TRP Q 197 " --> pdb=" O SER Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 229 Processing helix chain 'Q' and resid 244 through 273 removed outlier: 3.562A pdb=" N SER Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Proline residue: Q 263 - end of helix Processing helix chain 'Q' and resid 282 through 313 removed outlier: 3.528A pdb=" N PHE Q 286 " --> pdb=" O ASP Q 282 " (cutoff:3.500A) Proline residue: Q 292 - end of helix removed outlier: 4.079A pdb=" N SER Q 302 " --> pdb=" O SER Q 298 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS Q 303 " --> pdb=" O TYR Q 299 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Q 304 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN Q 305 " --> pdb=" O ASN Q 301 " (cutoff:3.500A) Proline residue: Q 306 - end of helix Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.224A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.855A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.363A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA3, first strand: chain 'Q' and resid 168 through 171 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'D' and resid 57 through 59 removed outlier: 4.973A pdb=" N MET D 34 " --> pdb=" O MET D 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.995A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 92 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N MET C 34 " --> pdb=" O MET C 51 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.624A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.556A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.868A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.306A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.703A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.701A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.655A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.782A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.418A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AC1, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.198A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1875 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: 2.16 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2021 1.30 - 1.43: 3596 1.43 - 1.56: 7569 1.56 - 1.70: 100 1.70 - 1.83: 144 Bond restraints: 13430 Sorted by residual: bond pdb=" C21 PCF R 401 " pdb=" O21 PCF R 401 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C21 PCF Q 401 " pdb=" O21 PCF Q 401 " ideal model delta sigma weight residual 1.334 1.431 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 PCF Q 401 " pdb=" O31 PCF Q 401 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C31 PCF R 401 " pdb=" O31 PCF R 401 " ideal model delta sigma weight residual 1.329 1.410 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.07e-02 8.73e+03 1.57e+01 ... (remaining 13425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 18153 4.63 - 9.27: 156 9.27 - 13.90: 8 13.90 - 18.54: 0 18.54 - 23.17: 2 Bond angle restraints: 18319 Sorted by residual: angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 120.03 128.64 -8.61 9.90e-01 1.02e+00 7.56e+01 angle pdb=" N ARG R 55 " pdb=" CA ARG R 55 " pdb=" C ARG R 55 " ideal model delta sigma weight residual 113.20 103.24 9.96 1.21e+00 6.83e-01 6.78e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 103.48 9.75 1.24e+00 6.50e-01 6.19e+01 angle pdb=" O12 PCF Q 401 " pdb=" P PCF Q 401 " pdb=" O14 PCF Q 401 " ideal model delta sigma weight residual 123.69 100.52 23.17 3.00e+00 1.11e-01 5.97e+01 angle pdb=" O12 PCF R 401 " pdb=" P PCF R 401 " pdb=" O14 PCF R 401 " ideal model delta sigma weight residual 123.69 101.07 22.62 3.00e+00 1.11e-01 5.68e+01 ... (remaining 18314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 7904 21.53 - 43.05: 506 43.05 - 64.58: 120 64.58 - 86.11: 10 86.11 - 107.63: 3 Dihedral angle restraints: 8543 sinusoidal: 3715 harmonic: 4828 Sorted by residual: dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N PRO C 41 " pdb=" CA PRO C 41 " ideal model delta harmonic sigma weight residual 180.00 136.71 43.29 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta harmonic sigma weight residual 180.00 139.55 40.45 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CB CYS D 33 " pdb=" SG CYS D 33 " pdb=" SG CYS D 110 " pdb=" CB CYS D 110 " ideal model delta sinusoidal sigma weight residual 93.00 156.18 -63.18 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 8540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1626 0.067 - 0.134: 359 0.134 - 0.202: 99 0.202 - 0.269: 33 0.269 - 0.336: 14 Chirality restraints: 2131 Sorted by residual: chirality pdb=" C17 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C16 CLR R 406 " pdb=" C20 CLR R 406 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C17 CLR Q 407 " pdb=" C13 CLR Q 407 " pdb=" C16 CLR Q 407 " pdb=" C20 CLR Q 407 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C17 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C16 CLR R 403 " pdb=" C20 CLR R 403 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2128 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLN B 75 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 305 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO R 306 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO R 306 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 306 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 274 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C THR B 274 " 0.040 2.00e-02 2.50e+03 pdb=" O THR B 274 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 275 " -0.014 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 724 2.72 - 3.27: 12970 3.27 - 3.81: 21587 3.81 - 4.36: 26879 4.36 - 4.90: 45419 Nonbonded interactions: 107579 Sorted by model distance: nonbonded pdb=" OH TYR R 299 " pdb=" OH TYR C 105 " model vdw 2.180 3.040 nonbonded pdb=" N GLU A 318 " pdb=" OE1 GLU A 318 " model vdw 2.266 3.120 nonbonded pdb=" O SER D 117 " pdb=" OG SER D 117 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD1 ASP A 341 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.299 3.040 ... (remaining 107574 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 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 or (resid 3 through 7 and (name N or name CA or name C or name O or \ name CB )) or (resid 8 through 19 and (name N or name CA or name C or name O or \ name CB )) or resid 20 or (resid 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 or (resid 27 and (name N or name CA or na \ me C or name O or name CB )) or resid 28 or (resid 29 and (name N or name CA or \ name C or name O or name CB )) or resid 30 through 33 or (resid 34 and (name N o \ r name CA or name C or name O or name CB )) or resid 35 or (resid 36 through 41 \ and (name N or name CA or name C or name O or name CB )) or (resid 42 through 46 \ and (name N or name CA or name C or name O or name CB )) or resid 47 through 49 \ or (resid 50 and (name N or name CA or name C or name O or name CB )) or resid \ 51 through 54 or (resid 55 and (name N or name CA or name C or name O or name CB \ )) or resid 56 through 58 or (resid 59 through 64 and (name N or name CA or nam \ e C or name O or name CB )) or resid 65 through 68 or (resid 69 and (name N or n \ ame CA or name C or name O or name CB )) or resid 70 through 71 or (resid 72 and \ (name N or name CA or name C or name O or name CB )) or resid 73 through 76 or \ (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 78 o \ r (resid 79 through 92 and (name N or name CA or name C or name O or name CB )) \ or resid 93 or (resid 94 and (name N or name CA or name C or name O or name CB ) \ ) or resid 95 through 103 or (resid 104 through 105 and (name N or name CA or na \ me C or name O or name CB )) or resid 106 through 113 or (resid 114 and (name N \ or name CA or name C or name O or name CB )) or resid 115 through 121 or (resid \ 122 and (name N or name CA or name C or name O or name CB )) or resid 123 throug \ h 126 or (resid 127 through 129 and (name N or name CA or name C or name O or na \ me CB )))) selection = chain 'D' } ncs_group { reference = (chain 'Q' and (resid 28 through 56 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 139 or (resid 140 through 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 174 or \ (resid 175 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 6 through 408)) selection = (chain 'R' and (resid 28 through 140 or (resid 141 through 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 173 or (resid 174 t \ hrough 175 and (name N or name CA or name C or name O or name CB )) or resid 176 \ through 230 or (resid 231 through 234 and (name N or name CA or name C or name \ O or name CB )) or resid 243 through 312 or (resid 313 and (name N or name CA or \ name C or name O or name CB )) or resid 401 through 408)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.100 13438 Z= 0.553 Angle : 1.142 23.174 18335 Z= 0.634 Chirality : 0.071 0.336 2131 Planarity : 0.005 0.085 2209 Dihedral : 14.442 107.634 5415 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.41 % Favored : 96.22 % Rotamer: Outliers : 0.54 % Allowed : 17.62 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.04 (0.20), residues: 1641 helix: 1.07 (0.21), residues: 606 sheet: 0.32 (0.26), residues: 361 loop : -1.07 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 314 TYR 0.034 0.002 TYR B 105 PHE 0.028 0.002 PHE R 54 TRP 0.017 0.002 TRP C 36 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.55 (13430) covalent geometry : angle 1.13982 / 0.63 (18319) SS BOND : bond 0.02667 / 1.61 ( 8) SS BOND : angle 2.84549 / 1.88 ( 16) hydrogen bonds : bond 0.16107 / 10.79 ( 677) hydrogen bonds : angle 6.47366 / 4.56 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 273 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8172 (tm) cc_final: 0.7950 (tp) REVERT: A 247 MET cc_start: 0.7635 (ptp) cc_final: 0.7269 (mmp) REVERT: R 34 ILE cc_start: 0.7319 (mp) cc_final: 0.7074 (mp) REVERT: R 55 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5539 (mmp80) REVERT: R 241 ARG cc_start: 0.6245 (tpt170) cc_final: 0.5933 (tpt170) REVERT: B 163 ASP cc_start: 0.6020 (p0) cc_final: 0.5432 (p0) REVERT: B 217 MET cc_start: 0.6487 (ptm) cc_final: 0.5826 (ttp) REVERT: B 220 GLN cc_start: 0.4203 (mt0) cc_final: 0.3888 (mt0) REVERT: B 251 ARG cc_start: 0.5147 (mtt-85) cc_final: 0.4592 (ttm-80) REVERT: B 331 SER cc_start: 0.6914 (t) cc_final: 0.6319 (t) REVERT: S 29 PHE cc_start: 0.6941 (t80) cc_final: 0.6518 (t80) REVERT: S 83 MET cc_start: 0.6227 (mtm) cc_final: 0.5503 (mtm) outliers start: 7 outliers final: 3 residues processed: 277 average time/residue: 0.1101 time to fit residues: 43.7229 Evaluate side-chains 234 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain C residue 70 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.238926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197739 restraints weight = 16029.937| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.90 r_work: 0.4076 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13438 Z= 0.149 Angle : 0.650 8.925 18335 Z= 0.324 Chirality : 0.044 0.183 2131 Planarity : 0.004 0.051 2209 Dihedral : 9.615 79.462 2824 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.68 % Favored : 97.01 % Rotamer: Outliers : 4.02 % Allowed : 15.92 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: 0.43 (0.21), residues: 1641 helix: 1.40 (0.21), residues: 613 sheet: 0.45 (0.26), residues: 368 loop : -0.83 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.017 0.002 TYR R 88 PHE 0.020 0.002 PHE B 199 TRP 0.021 0.002 TRP C 36 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13430) covalent geometry : angle 0.64885 / 0.32 (18319) SS BOND : bond 0.00319 / 0.20 ( 8) SS BOND : angle 1.25887 / 0.75 ( 16) hydrogen bonds : bond 0.04183 / 2.82 ( 677) hydrogen bonds : angle 4.83883 / 3.40 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.467 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: A 38 LEU cc_start: 0.8209 (tm) cc_final: 0.7991 (tp) REVERT: A 243 MET cc_start: 0.4609 (tmm) cc_final: 0.4288 (tmm) REVERT: A 248 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7953 (mptt) REVERT: R 75 ASP cc_start: 0.7530 (t70) cc_final: 0.7310 (t70) REVERT: R 162 MET cc_start: 0.7722 (mmm) cc_final: 0.7498 (mmm) REVERT: Q 221 TYR cc_start: 0.7537 (m-80) cc_final: 0.7319 (m-10) REVERT: Q 311 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5531 (t80) REVERT: C 36 TRP cc_start: 0.7612 (m100) cc_final: 0.7254 (m100) REVERT: B 163 ASP cc_start: 0.6839 (p0) cc_final: 0.6345 (p0) REVERT: B 217 MET cc_start: 0.7014 (ptm) cc_final: 0.6682 (ttp) REVERT: B 325 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6199 (ptm) REVERT: S 83 MET cc_start: 0.6003 (mtm) cc_final: 0.5714 (mtt) outliers start: 52 outliers final: 37 residues processed: 270 average time/residue: 0.1139 time to fit residues: 44.9523 Evaluate side-chains 272 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 311 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.236306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.194296 restraints weight = 16213.165| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.90 r_work: 0.4042 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13438 Z= 0.141 Angle : 0.606 9.813 18335 Z= 0.302 Chirality : 0.043 0.215 2131 Planarity : 0.004 0.047 2209 Dihedral : 9.273 70.798 2817 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.86 % Favored : 96.83 % Rotamer: Outliers : 4.17 % Allowed : 16.38 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1641 helix: 1.51 (0.21), residues: 615 sheet: 0.38 (0.25), residues: 380 loop : -0.73 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.017 0.002 TYR C 29 PHE 0.018 0.002 PHE Q 222 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13430) covalent geometry : angle 0.60497 / 0.30 (18319) SS BOND : bond 0.00327 / 0.20 ( 8) SS BOND : angle 1.09365 / 0.63 ( 16) hydrogen bonds : bond 0.03854 / 2.60 ( 677) hydrogen bonds : angle 4.58116 / 3.22 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7567 (mmmt) REVERT: A 198 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6923 (tmm) REVERT: A 248 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8198 (mttt) REVERT: A 275 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7719 (mm-30) REVERT: R 75 ASP cc_start: 0.7725 (t70) cc_final: 0.7496 (t70) REVERT: Q 264 TYR cc_start: 0.8210 (t80) cc_final: 0.7791 (t80) REVERT: B 68 ARG cc_start: 0.5152 (ttt180) cc_final: 0.4446 (ttt180) REVERT: B 163 ASP cc_start: 0.6632 (p0) cc_final: 0.6175 (p0) REVERT: B 217 MET cc_start: 0.6923 (ptm) cc_final: 0.6685 (ttp) REVERT: B 220 GLN cc_start: 0.5690 (mt0) cc_final: 0.5444 (mt0) REVERT: B 293 ASN cc_start: 0.7263 (m-40) cc_final: 0.6529 (p0) REVERT: S 83 MET cc_start: 0.6129 (mtm) cc_final: 0.5808 (mpp) outliers start: 54 outliers final: 42 residues processed: 275 average time/residue: 0.0974 time to fit residues: 40.3616 Evaluate side-chains 278 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 195 TRP Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 312 PHE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 204 SER Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 79 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.234730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.191979 restraints weight = 16107.465| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.01 r_work: 0.4025 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13438 Z= 0.134 Angle : 0.589 8.915 18335 Z= 0.295 Chirality : 0.042 0.193 2131 Planarity : 0.004 0.048 2209 Dihedral : 8.979 59.178 2817 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.80 % Favored : 96.89 % Rotamer: Outliers : 4.79 % Allowed : 16.38 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1641 helix: 1.58 (0.21), residues: 619 sheet: 0.51 (0.26), residues: 358 loop : -0.70 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR R 88 PHE 0.017 0.002 PHE B 234 TRP 0.024 0.002 TRP C 36 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13430) covalent geometry : angle 0.58810 / 0.29 (18319) SS BOND : bond 0.00293 / 0.18 ( 8) SS BOND : angle 1.26207 / 0.78 ( 16) hydrogen bonds : bond 0.03612 / 2.41 ( 677) hydrogen bonds : angle 4.49105 / 3.15 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7533 (mmmt) REVERT: A 198 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: A 208 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.7037 (ttm-80) REVERT: A 275 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 308 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7370 (mm-30) REVERT: R 75 ASP cc_start: 0.7829 (t70) cc_final: 0.7611 (t70) REVERT: Q 172 ASP cc_start: 0.7762 (t70) cc_final: 0.7521 (t70) REVERT: Q 264 TYR cc_start: 0.8267 (t80) cc_final: 0.7854 (t80) REVERT: Q 290 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8133 (tp) REVERT: C 57 THR cc_start: 0.8659 (p) cc_final: 0.8449 (p) REVERT: B 68 ARG cc_start: 0.5553 (ttt180) cc_final: 0.4571 (ttt180) REVERT: B 163 ASP cc_start: 0.6614 (p0) cc_final: 0.6268 (p0) REVERT: B 217 MET cc_start: 0.7032 (ptm) cc_final: 0.6721 (ttp) REVERT: B 220 GLN cc_start: 0.5764 (mt0) cc_final: 0.5445 (mt0) REVERT: B 293 ASN cc_start: 0.7256 (m-40) cc_final: 0.6516 (p0) REVERT: B 296 VAL cc_start: 0.6488 (t) cc_final: 0.6273 (m) REVERT: S 83 MET cc_start: 0.6181 (mtm) cc_final: 0.5823 (mpp) outliers start: 62 outliers final: 46 residues processed: 280 average time/residue: 0.0989 time to fit residues: 41.7220 Evaluate side-chains 286 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 312 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 204 SER Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.235341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.192751 restraints weight = 16177.708| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.11 r_work: 0.4023 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13438 Z= 0.124 Angle : 0.577 7.886 18335 Z= 0.289 Chirality : 0.042 0.192 2131 Planarity : 0.004 0.049 2209 Dihedral : 8.700 59.763 2815 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.07 % Rotamer: Outliers : 4.48 % Allowed : 16.62 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1641 helix: 1.66 (0.21), residues: 621 sheet: 0.53 (0.26), residues: 365 loop : -0.68 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.015 0.001 TYR R 88 PHE 0.016 0.001 PHE Q 214 TRP 0.028 0.001 TRP C 36 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13430) covalent geometry : angle 0.57624 / 0.29 (18319) SS BOND : bond 0.00268 / 0.16 ( 8) SS BOND : angle 1.16695 / 0.71 ( 16) hydrogen bonds : bond 0.03512 / 2.35 ( 677) hydrogen bonds : angle 4.40599 / 3.09 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7537 (mmmt) REVERT: A 257 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7873 (pmtt) REVERT: A 275 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 308 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7380 (mm-30) REVERT: R 34 ILE cc_start: 0.8637 (mp) cc_final: 0.8338 (mt) REVERT: R 75 ASP cc_start: 0.7940 (t70) cc_final: 0.7689 (t70) REVERT: R 245 ARG cc_start: 0.6164 (tpp-160) cc_final: 0.5677 (tpp-160) REVERT: Q 172 ASP cc_start: 0.7777 (t70) cc_final: 0.7561 (t70) REVERT: Q 264 TYR cc_start: 0.8285 (t80) cc_final: 0.7887 (t80) REVERT: Q 290 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 68 ARG cc_start: 0.5413 (ttt180) cc_final: 0.4398 (ttt180) REVERT: B 217 MET cc_start: 0.7175 (ptm) cc_final: 0.6792 (ttp) REVERT: B 220 GLN cc_start: 0.5751 (mt0) cc_final: 0.5401 (mt0) REVERT: B 234 PHE cc_start: 0.5534 (OUTLIER) cc_final: 0.4787 (m-10) REVERT: B 293 ASN cc_start: 0.7279 (m-40) cc_final: 0.6586 (p0) REVERT: S 83 MET cc_start: 0.6287 (mtm) cc_final: 0.5801 (mpp) outliers start: 58 outliers final: 47 residues processed: 284 average time/residue: 0.0965 time to fit residues: 41.0052 Evaluate side-chains 288 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain R residue 312 PHE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 204 SER Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 77 optimal weight: 0.0060 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.235605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193317 restraints weight = 16097.846| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.27 r_work: 0.4011 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13438 Z= 0.115 Angle : 0.575 8.482 18335 Z= 0.287 Chirality : 0.042 0.195 2131 Planarity : 0.004 0.049 2209 Dihedral : 8.485 58.994 2815 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.11 % Favored : 96.65 % Rotamer: Outliers : 4.48 % Allowed : 17.23 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1641 helix: 1.72 (0.21), residues: 621 sheet: 0.48 (0.26), residues: 369 loop : -0.64 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 127 TYR 0.013 0.001 TYR R 88 PHE 0.018 0.001 PHE Q 214 TRP 0.031 0.001 TRP C 36 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13430) covalent geometry : angle 0.57475 / 0.29 (18319) SS BOND : bond 0.00261 / 0.16 ( 8) SS BOND : angle 1.11300 / 0.69 ( 16) hydrogen bonds : bond 0.03388 / 2.27 ( 677) hydrogen bonds : angle 4.32947 / 3.03 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.492 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: A 197 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (mmmt) REVERT: A 198 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6963 (tmm) REVERT: A 257 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7887 (pmtt) REVERT: A 275 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 308 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7392 (mm-30) REVERT: R 34 ILE cc_start: 0.8622 (mp) cc_final: 0.8324 (mt) REVERT: R 75 ASP cc_start: 0.7988 (t70) cc_final: 0.7730 (t70) REVERT: R 165 MET cc_start: 0.8054 (tpp) cc_final: 0.7746 (ttm) REVERT: R 226 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6539 (tt0) REVERT: R 245 ARG cc_start: 0.6107 (tpp-160) cc_final: 0.5665 (tpp-160) REVERT: Q 264 TYR cc_start: 0.8296 (t80) cc_final: 0.7909 (t80) REVERT: Q 282 ASP cc_start: 0.7932 (p0) cc_final: 0.7655 (p0) REVERT: Q 290 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 68 ARG cc_start: 0.5505 (ttt180) cc_final: 0.4402 (ttt180) REVERT: B 163 ASP cc_start: 0.6566 (p0) cc_final: 0.6212 (p0) REVERT: B 217 MET cc_start: 0.7218 (ptm) cc_final: 0.6947 (ttp) REVERT: B 220 GLN cc_start: 0.5761 (mt0) cc_final: 0.5396 (mt0) REVERT: B 234 PHE cc_start: 0.5546 (OUTLIER) cc_final: 0.4764 (m-10) REVERT: B 293 ASN cc_start: 0.7424 (m-40) cc_final: 0.6695 (p0) REVERT: S 83 MET cc_start: 0.6265 (mtm) cc_final: 0.6045 (mtm) outliers start: 58 outliers final: 44 residues processed: 284 average time/residue: 0.1053 time to fit residues: 44.9588 Evaluate side-chains 287 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain R residue 312 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 125 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 301 ASN B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.227468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.184093 restraints weight = 16096.395| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.56 r_work: 0.3938 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13438 Z= 0.237 Angle : 0.720 10.484 18335 Z= 0.361 Chirality : 0.048 0.279 2131 Planarity : 0.005 0.053 2209 Dihedral : 9.084 56.228 2815 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.20 % Favored : 95.49 % Rotamer: Outliers : 5.33 % Allowed : 16.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1641 helix: 1.28 (0.21), residues: 616 sheet: 0.10 (0.26), residues: 387 loop : -0.85 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.024 0.002 TYR R 88 PHE 0.026 0.003 PHE R 78 TRP 0.042 0.002 TRP C 36 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (13430) covalent geometry : angle 0.71858 / 0.36 (18319) SS BOND : bond 0.00586 / 0.38 ( 8) SS BOND : angle 1.47226 / 0.90 ( 16) hydrogen bonds : bond 0.04165 / 2.77 ( 677) hydrogen bonds : angle 4.80494 / 3.38 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (mmmt) REVERT: A 243 MET cc_start: 0.5302 (tpp) cc_final: 0.5044 (tpp) REVERT: A 257 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8181 (pmtt) REVERT: A 275 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 296 TYR cc_start: 0.7616 (t80) cc_final: 0.7342 (t80) REVERT: R 34 ILE cc_start: 0.8705 (mp) cc_final: 0.8405 (mt) REVERT: R 75 ASP cc_start: 0.8046 (t70) cc_final: 0.7827 (t70) REVERT: R 262 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7372 (tmm) REVERT: Q 217 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: Q 264 TYR cc_start: 0.8393 (t80) cc_final: 0.8105 (t80) REVERT: Q 282 ASP cc_start: 0.7869 (p0) cc_final: 0.7579 (p0) REVERT: Q 290 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 68 ARG cc_start: 0.6069 (ttt180) cc_final: 0.5263 (mtp180) REVERT: B 217 MET cc_start: 0.7358 (ptm) cc_final: 0.6967 (ttp) REVERT: B 220 GLN cc_start: 0.5980 (mt0) cc_final: 0.5550 (mt0) REVERT: B 234 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.4309 (t80) REVERT: B 293 ASN cc_start: 0.7580 (m-40) cc_final: 0.6786 (p0) REVERT: S 60 TYR cc_start: 0.7750 (m-80) cc_final: 0.7163 (m-80) outliers start: 69 outliers final: 53 residues processed: 277 average time/residue: 0.1003 time to fit residues: 41.8575 Evaluate side-chains 294 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 204 SER Chi-restraints excluded: chain Q residue 217 MET Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 161 TYR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 138 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 41 optimal weight: 0.0020 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.233447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191708 restraints weight = 16000.638| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.92 r_work: 0.4029 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13438 Z= 0.112 Angle : 0.596 9.088 18335 Z= 0.298 Chirality : 0.042 0.192 2131 Planarity : 0.004 0.049 2209 Dihedral : 8.476 59.821 2815 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.68 % Favored : 97.14 % Rotamer: Outliers : 3.17 % Allowed : 19.01 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1641 helix: 1.58 (0.21), residues: 623 sheet: 0.38 (0.26), residues: 371 loop : -0.74 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 127 TYR 0.012 0.001 TYR C 79 PHE 0.019 0.001 PHE B 199 TRP 0.049 0.002 TRP C 36 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13430) covalent geometry : angle 0.59559 / 0.30 (18319) SS BOND : bond 0.00226 / 0.14 ( 8) SS BOND : angle 1.12907 / 0.75 ( 16) hydrogen bonds : bond 0.03432 / 2.29 ( 677) hydrogen bonds : angle 4.47425 / 3.15 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7587 (mmmt) REVERT: A 275 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 296 TYR cc_start: 0.7537 (t80) cc_final: 0.7235 (t80) REVERT: R 34 ILE cc_start: 0.8618 (mp) cc_final: 0.8330 (mt) REVERT: R 75 ASP cc_start: 0.8005 (t70) cc_final: 0.7756 (t70) REVERT: R 262 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7446 (tmm) REVERT: Q 264 TYR cc_start: 0.8400 (t80) cc_final: 0.8130 (t80) REVERT: Q 282 ASP cc_start: 0.7817 (p0) cc_final: 0.7539 (p0) REVERT: Q 290 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (tp) REVERT: B 68 ARG cc_start: 0.5835 (ttt180) cc_final: 0.5093 (mtp180) REVERT: B 199 PHE cc_start: 0.6026 (p90) cc_final: 0.5742 (p90) REVERT: B 217 MET cc_start: 0.7377 (ptm) cc_final: 0.6978 (ttp) REVERT: B 220 GLN cc_start: 0.5644 (mt0) cc_final: 0.5273 (mt0) REVERT: B 234 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.4758 (m-10) REVERT: B 293 ASN cc_start: 0.7556 (m-40) cc_final: 0.6870 (p0) REVERT: B 325 MET cc_start: 0.6589 (tpt) cc_final: 0.6338 (mmt) REVERT: S 60 TYR cc_start: 0.7597 (m-80) cc_final: 0.7369 (m-80) outliers start: 41 outliers final: 33 residues processed: 272 average time/residue: 0.1012 time to fit residues: 41.9472 Evaluate side-chains 276 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 128 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.231526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.188844 restraints weight = 16229.686| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.95 r_work: 0.3992 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13438 Z= 0.136 Angle : 0.610 8.627 18335 Z= 0.304 Chirality : 0.043 0.189 2131 Planarity : 0.004 0.050 2209 Dihedral : 8.380 59.708 2815 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 3.32 % Allowed : 18.93 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1641 helix: 1.61 (0.21), residues: 623 sheet: 0.27 (0.26), residues: 378 loop : -0.70 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 127 TYR 0.016 0.001 TYR S 103 PHE 0.018 0.002 PHE B 199 TRP 0.059 0.002 TRP C 36 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13430) covalent geometry : angle 0.60952 / 0.30 (18319) SS BOND : bond 0.00326 / 0.19 ( 8) SS BOND : angle 1.15683 / 0.73 ( 16) hydrogen bonds : bond 0.03485 / 2.33 ( 677) hydrogen bonds : angle 4.48443 / 3.15 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7842 (pmtt) REVERT: A 275 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 296 TYR cc_start: 0.7536 (t80) cc_final: 0.7293 (t80) REVERT: R 34 ILE cc_start: 0.8622 (mp) cc_final: 0.8333 (mt) REVERT: R 75 ASP cc_start: 0.8039 (t70) cc_final: 0.7820 (t70) REVERT: R 262 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7493 (tmm) REVERT: Q 217 MET cc_start: 0.7878 (mmp) cc_final: 0.7395 (mmm) REVERT: Q 264 TYR cc_start: 0.8438 (t80) cc_final: 0.8178 (t80) REVERT: Q 272 MET cc_start: 0.7364 (ttt) cc_final: 0.7148 (ttt) REVERT: Q 282 ASP cc_start: 0.7801 (p0) cc_final: 0.7523 (p0) REVERT: Q 290 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (tp) REVERT: B 68 ARG cc_start: 0.5962 (ttt180) cc_final: 0.5467 (mtp-110) REVERT: B 199 PHE cc_start: 0.6083 (p90) cc_final: 0.5772 (p90) REVERT: B 217 MET cc_start: 0.7408 (ptm) cc_final: 0.6995 (ttp) REVERT: B 220 GLN cc_start: 0.5713 (mt0) cc_final: 0.5317 (mt0) REVERT: B 234 PHE cc_start: 0.5557 (OUTLIER) cc_final: 0.4739 (m-10) REVERT: B 293 ASN cc_start: 0.7572 (m-40) cc_final: 0.6908 (p0) REVERT: B 325 MET cc_start: 0.6636 (tpt) cc_final: 0.6329 (mmt) outliers start: 43 outliers final: 36 residues processed: 266 average time/residue: 0.0955 time to fit residues: 38.5359 Evaluate side-chains 281 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 273 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 120 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.230271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188098 restraints weight = 16133.869| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.20 r_work: 0.3954 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13438 Z= 0.158 Angle : 0.641 11.887 18335 Z= 0.318 Chirality : 0.045 0.229 2131 Planarity : 0.004 0.051 2209 Dihedral : 8.408 59.482 2815 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.66 % Favored : 96.10 % Rotamer: Outliers : 3.40 % Allowed : 19.09 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1641 helix: 1.57 (0.21), residues: 621 sheet: 0.25 (0.26), residues: 376 loop : -0.75 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 127 TYR 0.017 0.002 TYR R 88 PHE 0.019 0.002 PHE B 234 TRP 0.073 0.002 TRP C 36 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (13430) covalent geometry : angle 0.63991 / 0.32 (18319) SS BOND : bond 0.00368 / 0.22 ( 8) SS BOND : angle 1.29528 / 0.84 ( 16) hydrogen bonds : bond 0.03606 / 2.40 ( 677) hydrogen bonds : angle 4.56221 / 3.22 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8038 (mttp) cc_final: 0.7832 (mttp) REVERT: A 257 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (pmtt) REVERT: A 275 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 296 TYR cc_start: 0.7608 (t80) cc_final: 0.7382 (t80) REVERT: R 34 ILE cc_start: 0.8655 (mp) cc_final: 0.8356 (mt) REVERT: R 75 ASP cc_start: 0.8051 (t70) cc_final: 0.7834 (t70) REVERT: R 262 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: Q 217 MET cc_start: 0.7956 (mmp) cc_final: 0.7416 (mmm) REVERT: Q 282 ASP cc_start: 0.7780 (p0) cc_final: 0.7498 (p0) REVERT: Q 290 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8313 (tp) REVERT: B 68 ARG cc_start: 0.6057 (ttt180) cc_final: 0.5417 (mtp180) REVERT: B 199 PHE cc_start: 0.6067 (p90) cc_final: 0.5792 (p90) REVERT: B 214 ARG cc_start: 0.8005 (mpt180) cc_final: 0.7791 (mpt180) REVERT: B 217 MET cc_start: 0.7409 (ptm) cc_final: 0.6995 (ttp) REVERT: B 220 GLN cc_start: 0.5729 (mt0) cc_final: 0.5347 (mt0) REVERT: B 234 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.4742 (m-10) REVERT: B 246 ASP cc_start: 0.7446 (m-30) cc_final: 0.7121 (t0) REVERT: B 293 ASN cc_start: 0.7645 (m-40) cc_final: 0.6977 (p0) REVERT: B 325 MET cc_start: 0.6561 (tpt) cc_final: 0.6282 (mmt) REVERT: S 93 MET cc_start: 0.6853 (tpp) cc_final: 0.6562 (tpp) REVERT: S 218 MET cc_start: 0.6604 (ttp) cc_final: 0.6309 (ttp) outliers start: 44 outliers final: 36 residues processed: 262 average time/residue: 0.0897 time to fit residues: 35.3311 Evaluate side-chains 277 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 162 MET Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 0.0670 chunk 50 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 156 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.234491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190578 restraints weight = 16063.816| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.11 r_work: 0.4014 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13438 Z= 0.108 Angle : 0.601 11.255 18335 Z= 0.296 Chirality : 0.042 0.224 2131 Planarity : 0.004 0.048 2209 Dihedral : 8.093 59.498 2815 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.99 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 19.71 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1641 helix: 1.72 (0.21), residues: 621 sheet: 0.60 (0.27), residues: 338 loop : -0.79 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 127 TYR 0.012 0.001 TYR C 79 PHE 0.017 0.001 PHE B 199 TRP 0.078 0.002 TRP C 36 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13430) covalent geometry : angle 0.60000 / 0.30 (18319) SS BOND : bond 0.00286 / 0.18 ( 8) SS BOND : angle 1.18736 / 0.81 ( 16) hydrogen bonds : bond 0.03320 / 2.21 ( 677) hydrogen bonds : angle 4.41648 / 3.12 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3448.58 seconds wall clock time: 59 minutes 48.25 seconds (3588.25 seconds total)