Starting phenix.real_space_refine on Wed Mar 4 05:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lfo_0879/03_2026/6lfo_0879.map" } resolution = 3.4 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6128 2.51 5 N 1632 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9573 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 525 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "R" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2451 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.23 Number of scatterers: 9573 At special positions: 0 Unit cell: (87.36, 122.027, 155.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1745 8.00 N 1632 7.00 C 6128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.01 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.04 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.04 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 458.8 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 17 sheets defined 35.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 25 removed outlier: 3.678A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.562A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.398A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.063A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.662A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 4.426A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.987A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.027A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.769A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.526A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.863A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.675A pdb=" N VAL D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 46 removed outlier: 4.194A pdb=" N GLU R 45 " --> pdb=" O GLU R 42 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE R 46 " --> pdb=" O SER R 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 42 through 46' Processing helix chain 'R' and resid 47 through 75 removed outlier: 3.756A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 98 removed outlier: 4.223A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.892A pdb=" N VAL R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 136 removed outlier: 4.202A pdb=" N CYS R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 134 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 147 removed outlier: 3.546A pdb=" N SER R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 161 removed outlier: 4.503A pdb=" N ARG R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 183 removed outlier: 3.520A pdb=" N LEU R 175 " --> pdb=" O GLY R 171 " (cutoff:3.500A) Proline residue: R 179 - end of helix removed outlier: 3.743A pdb=" N PHE R 183 " --> pdb=" O PRO R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 219 removed outlier: 3.949A pdb=" N LEU R 210 " --> pdb=" O ASN R 206 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 220 through 228 Processing helix chain 'R' and resid 230 through 241 removed outlier: 3.540A pdb=" N PHE R 239 " --> pdb=" O LEU R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 264 removed outlier: 3.559A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG R 251 " --> pdb=" O HIS R 247 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 279 removed outlier: 3.533A pdb=" N VAL R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU R 272 " --> pdb=" O ASN R 268 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 305 removed outlier: 4.170A pdb=" N ALA R 298 " --> pdb=" O ARG R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 315 Processing helix chain 'R' and resid 318 through 332 removed outlier: 4.117A pdb=" N LEU R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS R 327 " --> pdb=" O HIS R 323 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.848A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.672A 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 removed outlier: 3.798A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.985A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.758A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.176A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.900A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.753A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.242A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.788A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.379A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.575A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AB1, first strand: chain 'R' and resid 184 through 185 removed outlier: 3.513A pdb=" N ARG R 185 " --> pdb=" O TYR R 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.923A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.978A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 174 through 175 Processing sheet with id=AB8, first strand: chain 'S' and resid 177 through 178 removed outlier: 3.662A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1035 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: 1.46 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2964 1.33 - 1.46: 2130 1.46 - 1.58: 4581 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9771 Sorted by residual: bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.89e+00 bond pdb=" CB VAL S 97 " pdb=" CG2 VAL S 97 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.28e+00 bond pdb=" CB TRP S 47 " pdb=" CG TRP S 47 " ideal model delta sigma weight residual 1.498 1.416 0.082 3.10e-02 1.04e+03 7.01e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.55e+00 bond pdb=" CG LEU B 168 " pdb=" CD1 LEU B 168 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 12910 3.00 - 6.01: 297 6.01 - 9.01: 30 9.01 - 12.01: 9 12.01 - 15.01: 2 Bond angle restraints: 13248 Sorted by residual: angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" CA LEU R 44 " pdb=" CB LEU R 44 " pdb=" CG LEU R 44 " ideal model delta sigma weight residual 116.30 131.31 -15.01 3.50e+00 8.16e-02 1.84e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5171 17.97 - 35.93: 591 35.93 - 53.90: 90 53.90 - 71.86: 15 71.86 - 89.83: 8 Dihedral angle restraints: 5875 sinusoidal: 2309 harmonic: 3566 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -134.87 -45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 34 " pdb=" CB CYS D 34 " ideal model delta sinusoidal sigma weight residual -86.00 -143.72 57.72 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1113 0.064 - 0.128: 356 0.128 - 0.192: 49 0.192 - 0.257: 11 0.257 - 0.321: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB THR A 181 " pdb=" CA THR A 181 " pdb=" OG1 THR A 181 " pdb=" CG2 THR A 181 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA MET A 240 " pdb=" N MET A 240 " pdb=" C MET A 240 " pdb=" CB MET A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1528 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 31 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 178 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C TYR S 178 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR S 178 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG S 179 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 112 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.44e+00 pdb=" CG TRP R 112 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 112 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP R 112 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 112 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 112 " 0.003 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2646 2.78 - 3.31: 8372 3.31 - 3.84: 15614 3.84 - 4.37: 17999 4.37 - 4.90: 31225 Nonbonded interactions: 75856 Sorted by model distance: nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.255 3.040 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 228 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.305 3.120 nonbonded pdb=" OG SER S 149 " pdb=" N SER S 150 " model vdw 2.308 3.120 ... (remaining 75851 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.940 Find NCS groups from input model: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.013 0.116 9777 Z= 0.570 Angle : 1.134 15.015 13260 Z= 0.595 Chirality : 0.062 0.321 1531 Planarity : 0.007 0.107 1660 Dihedral : 15.003 89.828 3553 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.29 % Allowed : 11.96 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.54 (0.17), residues: 1212 helix: -4.48 (0.11), residues: 387 sheet: -3.37 (0.26), residues: 270 loop : -3.08 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 242 TYR 0.033 0.003 TYR S 178 PHE 0.023 0.003 PHE B 235 TRP 0.035 0.004 TRP R 112 HIS 0.010 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.01281 ( 9771) covalent geometry : angle 1.13316 (13248) SS BOND : bond 0.01034 ( 6) SS BOND : angle 1.68996 ( 12) hydrogen bonds : bond 0.29978 ( 358) hydrogen bonds : angle 10.83373 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7603 (mtm110) REVERT: A 35 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8457 (mttm) REVERT: A 232 LEU cc_start: 0.8521 (tt) cc_final: 0.7605 (tt) REVERT: A 243 MET cc_start: 0.8964 (tpp) cc_final: 0.8727 (mmm) REVERT: A 341 ASP cc_start: 0.7813 (t70) cc_final: 0.7427 (t0) REVERT: B 15 LYS cc_start: 0.9199 (tptt) cc_final: 0.8691 (ttmm) REVERT: B 157 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 188 MET cc_start: 0.8492 (mmm) cc_final: 0.7976 (mpp) REVERT: B 209 LYS cc_start: 0.8812 (mttm) cc_final: 0.8527 (mttt) REVERT: B 210 LEU cc_start: 0.9183 (tp) cc_final: 0.8927 (tt) REVERT: B 223 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 339 TRP cc_start: 0.8429 (m100) cc_final: 0.8143 (m100) REVERT: R 55 TYR cc_start: 0.8706 (m-80) cc_final: 0.8175 (m-80) REVERT: R 63 LEU cc_start: 0.7965 (mm) cc_final: 0.7567 (mm) REVERT: R 90 LEU cc_start: 0.8649 (tp) cc_final: 0.8381 (tp) REVERT: R 103 ILE cc_start: 0.7650 (mp) cc_final: 0.7443 (mp) REVERT: R 131 TYR cc_start: 0.7500 (m-80) cc_final: 0.7289 (m-10) REVERT: R 134 ILE cc_start: 0.8190 (mm) cc_final: 0.7933 (mm) REVERT: R 145 TYR cc_start: 0.8994 (t80) cc_final: 0.8756 (t80) REVERT: R 209 MET cc_start: 0.7637 (mmm) cc_final: 0.6987 (mmm) REVERT: R 227 MET cc_start: 0.7959 (mtp) cc_final: 0.7710 (mtp) REVERT: S 3 GLN cc_start: 0.7864 (pt0) cc_final: 0.7545 (pt0) REVERT: S 13 GLN cc_start: 0.8432 (mm110) cc_final: 0.7988 (pp30) REVERT: S 68 PHE cc_start: 0.8922 (m-10) cc_final: 0.8552 (m-10) REVERT: S 219 GLN cc_start: 0.8968 (pp30) cc_final: 0.8562 (pp30) outliers start: 3 outliers final: 0 residues processed: 309 average time/residue: 0.1214 time to fit residues: 49.1055 Evaluate side-chains 225 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 213 HIS B 62 HIS B 91 HIS B 119 ASN B 220 GLN B 340 ASN D 8 GLN R 66 ASN R 89 ASN ** R 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN R 310 ASN R 332 HIS S 39 GLN S 167 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119683 restraints weight = 14466.467| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.84 r_work: 0.3415 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9777 Z= 0.143 Angle : 0.660 8.672 13260 Z= 0.342 Chirality : 0.043 0.168 1531 Planarity : 0.005 0.091 1660 Dihedral : 5.969 39.172 1395 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.92 % Allowed : 18.58 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.20), residues: 1212 helix: -2.72 (0.20), residues: 399 sheet: -2.91 (0.27), residues: 292 loop : -2.72 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.025 0.001 TYR S 178 PHE 0.010 0.001 PHE S 27 TRP 0.023 0.001 TRP R 112 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9771) covalent geometry : angle 0.65867 (13248) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.61528 ( 12) hydrogen bonds : bond 0.04309 ( 358) hydrogen bonds : angle 5.83633 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7576 (mtm110) REVERT: A 296 TYR cc_start: 0.8529 (t80) cc_final: 0.8321 (t80) REVERT: A 304 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 310 LEU cc_start: 0.8914 (mt) cc_final: 0.8532 (mt) REVERT: B 9 GLN cc_start: 0.8281 (mm110) cc_final: 0.7967 (mp10) REVERT: B 15 LYS cc_start: 0.9110 (tptt) cc_final: 0.8793 (mtpp) REVERT: B 17 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 129 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7575 (mmm160) REVERT: B 292 PHE cc_start: 0.8029 (m-10) cc_final: 0.7626 (m-80) REVERT: B 297 TRP cc_start: 0.8856 (m100) cc_final: 0.8647 (m100) REVERT: C 38 MET cc_start: 0.8858 (ttp) cc_final: 0.8641 (ttp) REVERT: C 47 GLU cc_start: 0.7832 (mp0) cc_final: 0.7279 (mp0) REVERT: D 39 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6424 (tp) REVERT: R 63 LEU cc_start: 0.7881 (mm) cc_final: 0.7481 (mm) REVERT: R 134 ILE cc_start: 0.8485 (mm) cc_final: 0.8282 (mm) REVERT: R 173 SER cc_start: 0.9146 (t) cc_final: 0.8928 (p) REVERT: R 209 MET cc_start: 0.7623 (mmm) cc_final: 0.7095 (mmm) REVERT: R 226 ILE cc_start: 0.9221 (tt) cc_final: 0.8879 (tt) REVERT: R 242 HIS cc_start: 0.7809 (p90) cc_final: 0.7545 (p-80) REVERT: S 3 GLN cc_start: 0.8192 (pt0) cc_final: 0.7922 (pt0) REVERT: S 20 LEU cc_start: 0.7702 (mt) cc_final: 0.7411 (mt) REVERT: S 219 GLN cc_start: 0.9095 (pp30) cc_final: 0.8657 (pp30) REVERT: S 232 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7931 (ttpp) outliers start: 30 outliers final: 13 residues processed: 303 average time/residue: 0.0945 time to fit residues: 39.4275 Evaluate side-chains 248 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 144 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN D 8 GLN ** R 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119649 restraints weight = 14409.070| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.95 r_work: 0.3368 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9777 Z= 0.164 Angle : 0.651 8.747 13260 Z= 0.330 Chirality : 0.043 0.150 1531 Planarity : 0.004 0.089 1660 Dihedral : 5.451 37.002 1392 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.57 % Allowed : 19.75 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.43 (0.22), residues: 1212 helix: -1.70 (0.23), residues: 410 sheet: -2.64 (0.28), residues: 283 loop : -2.38 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.025 0.001 TYR S 178 PHE 0.016 0.001 PHE R 130 TRP 0.021 0.002 TRP R 112 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9771) covalent geometry : angle 0.65001 (13248) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.26604 ( 12) hydrogen bonds : bond 0.03471 ( 358) hydrogen bonds : angle 4.99391 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7714 (mtm110) REVERT: A 243 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 304 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 310 LEU cc_start: 0.9125 (mt) cc_final: 0.8651 (mt) REVERT: A 341 ASP cc_start: 0.8778 (t70) cc_final: 0.8361 (t0) REVERT: B 15 LYS cc_start: 0.9031 (tptt) cc_final: 0.8603 (ttmm) REVERT: B 17 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8276 (tm-30) REVERT: B 129 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7488 (mmm160) REVERT: B 188 MET cc_start: 0.8961 (mmm) cc_final: 0.8757 (tpp) REVERT: C 27 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7651 (mtt90) REVERT: C 47 GLU cc_start: 0.7923 (mp0) cc_final: 0.7351 (mp0) REVERT: D 39 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6333 (tp) REVERT: R 63 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7562 (mm) REVERT: R 95 LEU cc_start: 0.8546 (tp) cc_final: 0.8193 (pp) REVERT: R 126 LYS cc_start: 0.7402 (ttmm) cc_final: 0.6650 (ttpt) REVERT: R 209 MET cc_start: 0.7730 (mmm) cc_final: 0.7236 (mmm) REVERT: R 216 GLN cc_start: 0.8052 (tp40) cc_final: 0.6838 (tm-30) REVERT: R 226 ILE cc_start: 0.9194 (tt) cc_final: 0.8845 (tt) REVERT: R 242 HIS cc_start: 0.7803 (p90) cc_final: 0.7382 (p-80) REVERT: S 3 GLN cc_start: 0.8145 (pt0) cc_final: 0.7899 (pt0) REVERT: S 91 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7972 (t) REVERT: S 219 GLN cc_start: 0.9209 (pp30) cc_final: 0.8730 (pp30) REVERT: S 232 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7823 (ttpp) outliers start: 47 outliers final: 27 residues processed: 270 average time/residue: 0.0932 time to fit residues: 35.3907 Evaluate side-chains 262 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN R 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116756 restraints weight = 14692.463| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.84 r_work: 0.3384 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9777 Z= 0.153 Angle : 0.628 8.881 13260 Z= 0.317 Chirality : 0.042 0.161 1531 Planarity : 0.004 0.088 1660 Dihedral : 5.195 35.522 1392 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.25 % Allowed : 20.91 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.23), residues: 1212 helix: -1.11 (0.25), residues: 407 sheet: -2.34 (0.28), residues: 290 loop : -2.18 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.025 0.001 TYR S 178 PHE 0.017 0.001 PHE R 130 TRP 0.020 0.002 TRP R 112 HIS 0.003 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9771) covalent geometry : angle 0.62706 (13248) SS BOND : bond 0.00207 ( 6) SS BOND : angle 1.08410 ( 12) hydrogen bonds : bond 0.03103 ( 358) hydrogen bonds : angle 4.68982 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7676 (mtm110) REVERT: A 243 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8111 (mmm) REVERT: A 277 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7677 (ttmt) REVERT: A 304 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 310 LEU cc_start: 0.9160 (mt) cc_final: 0.8676 (mt) REVERT: B 9 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7741 (mp10) REVERT: B 15 LYS cc_start: 0.9042 (tptt) cc_final: 0.8580 (ttmm) REVERT: B 17 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 129 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.7528 (mmm160) REVERT: B 134 ARG cc_start: 0.8755 (ptt-90) cc_final: 0.8541 (ptt-90) REVERT: B 210 LEU cc_start: 0.9352 (tp) cc_final: 0.9117 (tp) REVERT: B 215 GLU cc_start: 0.8661 (mp0) cc_final: 0.8404 (mp0) REVERT: B 258 ASP cc_start: 0.7389 (t0) cc_final: 0.7180 (t0) REVERT: B 275 SER cc_start: 0.8823 (m) cc_final: 0.8576 (m) REVERT: B 292 PHE cc_start: 0.8146 (m-80) cc_final: 0.7563 (m-80) REVERT: B 325 MET cc_start: 0.8836 (tpp) cc_final: 0.8481 (tpp) REVERT: C 11 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 22 GLU cc_start: 0.7673 (tp30) cc_final: 0.7387 (tp30) REVERT: C 47 GLU cc_start: 0.7895 (mp0) cc_final: 0.7395 (mp0) REVERT: R 63 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7371 (mm) REVERT: R 95 LEU cc_start: 0.8491 (tp) cc_final: 0.8159 (pp) REVERT: R 126 LYS cc_start: 0.7568 (ttmm) cc_final: 0.6878 (ttpt) REVERT: R 137 LEU cc_start: 0.8404 (mp) cc_final: 0.8154 (mp) REVERT: R 209 MET cc_start: 0.7691 (mmm) cc_final: 0.7204 (mmm) REVERT: R 216 GLN cc_start: 0.7885 (tp40) cc_final: 0.7169 (tm-30) REVERT: R 226 ILE cc_start: 0.9098 (tt) cc_final: 0.8745 (tt) REVERT: S 3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7966 (pt0) REVERT: S 91 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7939 (t) REVERT: S 219 GLN cc_start: 0.9228 (pp30) cc_final: 0.8775 (pp30) REVERT: S 232 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7665 (ttpp) outliers start: 54 outliers final: 34 residues processed: 287 average time/residue: 0.0949 time to fit residues: 38.2413 Evaluate side-chains 262 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119993 restraints weight = 14559.942| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.88 r_work: 0.3423 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9777 Z= 0.110 Angle : 0.603 8.301 13260 Z= 0.301 Chirality : 0.041 0.144 1531 Planarity : 0.004 0.087 1660 Dihedral : 4.935 35.073 1392 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.47 % Allowed : 23.64 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.23), residues: 1212 helix: -0.64 (0.25), residues: 404 sheet: -2.00 (0.29), residues: 295 loop : -2.08 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.022 0.001 TYR S 178 PHE 0.014 0.001 PHE R 130 TRP 0.017 0.001 TRP S 111 HIS 0.005 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9771) covalent geometry : angle 0.60266 (13248) SS BOND : bond 0.00757 ( 6) SS BOND : angle 0.96578 ( 12) hydrogen bonds : bond 0.02868 ( 358) hydrogen bonds : angle 4.41062 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8290 (mtt-85) cc_final: 0.7569 (mtm110) REVERT: A 216 GLU cc_start: 0.8305 (tt0) cc_final: 0.7945 (tt0) REVERT: A 243 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8199 (mmm) REVERT: A 277 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7778 (ttmt) REVERT: A 304 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 9 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7985 (mp10) REVERT: B 15 LYS cc_start: 0.8997 (tptt) cc_final: 0.8561 (ttmm) REVERT: B 17 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 61 MET cc_start: 0.8841 (ppp) cc_final: 0.8298 (ppp) REVERT: B 129 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7528 (mmm160) REVERT: B 210 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9060 (tp) REVERT: B 211 TRP cc_start: 0.9271 (m100) cc_final: 0.8953 (m100) REVERT: B 215 GLU cc_start: 0.8772 (mp0) cc_final: 0.8506 (mp0) REVERT: B 262 MET cc_start: 0.8564 (mtp) cc_final: 0.8331 (mtp) REVERT: B 275 SER cc_start: 0.8760 (m) cc_final: 0.8485 (m) REVERT: B 292 PHE cc_start: 0.7954 (m-80) cc_final: 0.7405 (m-80) REVERT: B 297 TRP cc_start: 0.8933 (m100) cc_final: 0.8718 (m100) REVERT: B 325 MET cc_start: 0.8812 (tpp) cc_final: 0.8468 (tpp) REVERT: C 11 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8805 (tm-30) REVERT: R 63 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7368 (mm) REVERT: R 95 LEU cc_start: 0.8447 (tp) cc_final: 0.8201 (pp) REVERT: R 126 LYS cc_start: 0.7183 (ttmm) cc_final: 0.6563 (ttpt) REVERT: R 183 PHE cc_start: 0.8713 (m-80) cc_final: 0.8322 (m-80) REVERT: R 209 MET cc_start: 0.7659 (mmm) cc_final: 0.7260 (mmm) REVERT: R 216 GLN cc_start: 0.7712 (tp40) cc_final: 0.6940 (pp30) REVERT: R 226 ILE cc_start: 0.9060 (tt) cc_final: 0.8723 (tt) REVERT: R 293 ASP cc_start: 0.9156 (t0) cc_final: 0.8876 (t0) REVERT: S 3 GLN cc_start: 0.8288 (pt0) cc_final: 0.8031 (pt0) REVERT: S 86 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8863 (pp) REVERT: S 91 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8005 (t) REVERT: S 219 GLN cc_start: 0.9214 (pp30) cc_final: 0.8757 (pp30) outliers start: 46 outliers final: 23 residues processed: 288 average time/residue: 0.1006 time to fit residues: 40.3277 Evaluate side-chains 261 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN R 247 HIS S 39 GLN ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118996 restraints weight = 14416.970| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.81 r_work: 0.3406 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9777 Z= 0.131 Angle : 0.623 8.956 13260 Z= 0.311 Chirality : 0.042 0.162 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.897 34.239 1392 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.18 % Allowed : 24.03 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1212 helix: -0.44 (0.26), residues: 404 sheet: -1.87 (0.29), residues: 288 loop : -2.00 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.025 0.001 TYR S 178 PHE 0.014 0.001 PHE S 200 TRP 0.042 0.002 TRP R 112 HIS 0.004 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9771) covalent geometry : angle 0.62288 (13248) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.03253 ( 12) hydrogen bonds : bond 0.02864 ( 358) hydrogen bonds : angle 4.34678 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.7638 (mtm110) REVERT: A 216 GLU cc_start: 0.8334 (tt0) cc_final: 0.7968 (tt0) REVERT: A 277 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7828 (ttmt) REVERT: A 304 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 15 LYS cc_start: 0.9071 (tptt) cc_final: 0.8620 (ttmm) REVERT: B 17 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 61 MET cc_start: 0.8845 (ppp) cc_final: 0.8205 (ppp) REVERT: B 129 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7544 (mmm160) REVERT: B 210 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9057 (tp) REVERT: B 215 GLU cc_start: 0.8671 (mp0) cc_final: 0.8444 (mp0) REVERT: B 262 MET cc_start: 0.8515 (mtp) cc_final: 0.8239 (mtp) REVERT: B 275 SER cc_start: 0.8821 (m) cc_final: 0.8603 (m) REVERT: B 292 PHE cc_start: 0.8035 (m-80) cc_final: 0.7482 (m-80) REVERT: B 325 MET cc_start: 0.8871 (tpp) cc_final: 0.8533 (tpp) REVERT: C 11 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8813 (tm-30) REVERT: C 22 GLU cc_start: 0.7551 (tp30) cc_final: 0.7203 (tp30) REVERT: R 63 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7380 (mm) REVERT: R 95 LEU cc_start: 0.8460 (tp) cc_final: 0.8196 (pp) REVERT: R 126 LYS cc_start: 0.7120 (ttmm) cc_final: 0.6639 (tppt) REVERT: R 137 LEU cc_start: 0.8329 (mp) cc_final: 0.8079 (mp) REVERT: R 209 MET cc_start: 0.7672 (mmm) cc_final: 0.7260 (mmm) REVERT: R 216 GLN cc_start: 0.7706 (tp40) cc_final: 0.7094 (pp30) REVERT: R 226 ILE cc_start: 0.9057 (tt) cc_final: 0.8727 (tt) REVERT: R 293 ASP cc_start: 0.9146 (t0) cc_final: 0.8868 (t0) REVERT: S 3 GLN cc_start: 0.8142 (pt0) cc_final: 0.7907 (pt0) REVERT: S 86 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8847 (pp) REVERT: S 91 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8035 (t) REVERT: S 219 GLN cc_start: 0.9204 (pp30) cc_final: 0.8751 (pp30) outliers start: 43 outliers final: 33 residues processed: 274 average time/residue: 0.0973 time to fit residues: 37.3613 Evaluate side-chains 271 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118506 restraints weight = 14474.225| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.65 r_work: 0.3423 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9777 Z= 0.134 Angle : 0.631 10.327 13260 Z= 0.313 Chirality : 0.043 0.286 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.863 34.316 1392 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.67 % Allowed : 24.61 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.24), residues: 1212 helix: -0.24 (0.26), residues: 404 sheet: -1.81 (0.29), residues: 290 loop : -1.87 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.025 0.001 TYR S 178 PHE 0.019 0.001 PHE S 68 TRP 0.033 0.002 TRP R 112 HIS 0.004 0.001 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9771) covalent geometry : angle 0.63114 (13248) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.92830 ( 12) hydrogen bonds : bond 0.02859 ( 358) hydrogen bonds : angle 4.33221 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7388 (mtm110) REVERT: A 277 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7847 (ttmt) REVERT: A 304 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 15 LYS cc_start: 0.9049 (tptt) cc_final: 0.8579 (ttmm) REVERT: B 17 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 61 MET cc_start: 0.8757 (ppp) cc_final: 0.8162 (ppp) REVERT: B 129 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7542 (mmm160) REVERT: B 134 ARG cc_start: 0.8690 (ptt-90) cc_final: 0.8299 (ptt-90) REVERT: B 172 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: B 210 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9054 (tp) REVERT: B 275 SER cc_start: 0.8817 (m) cc_final: 0.8602 (m) REVERT: B 292 PHE cc_start: 0.7993 (m-80) cc_final: 0.7448 (m-80) REVERT: B 297 TRP cc_start: 0.8917 (m100) cc_final: 0.8710 (m100) REVERT: B 322 ASP cc_start: 0.8427 (t0) cc_final: 0.8220 (t0) REVERT: B 325 MET cc_start: 0.8860 (tpp) cc_final: 0.8572 (tpp) REVERT: C 11 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8780 (tm-30) REVERT: C 22 GLU cc_start: 0.7394 (tp30) cc_final: 0.7140 (tp30) REVERT: R 63 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7386 (mm) REVERT: R 126 LYS cc_start: 0.6983 (ttmm) cc_final: 0.6280 (ttpt) REVERT: R 209 MET cc_start: 0.7671 (mmm) cc_final: 0.7244 (mmm) REVERT: R 216 GLN cc_start: 0.8124 (tp40) cc_final: 0.7330 (tm-30) REVERT: R 226 ILE cc_start: 0.9111 (tt) cc_final: 0.8779 (tt) REVERT: R 293 ASP cc_start: 0.9088 (t0) cc_final: 0.8791 (t0) REVERT: S 3 GLN cc_start: 0.7993 (pt0) cc_final: 0.7748 (pt0) REVERT: S 20 LEU cc_start: 0.7599 (mm) cc_final: 0.7301 (mp) REVERT: S 86 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8878 (pp) REVERT: S 91 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.7965 (t) REVERT: S 219 GLN cc_start: 0.9142 (pp30) cc_final: 0.8773 (pp30) outliers start: 48 outliers final: 37 residues processed: 270 average time/residue: 0.1005 time to fit residues: 37.9008 Evaluate side-chains 260 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121927 restraints weight = 14404.346| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.71 r_work: 0.3455 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9777 Z= 0.117 Angle : 0.625 10.455 13260 Z= 0.310 Chirality : 0.042 0.256 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.764 33.968 1392 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.38 % Allowed : 24.51 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1212 helix: -0.05 (0.26), residues: 400 sheet: -1.68 (0.30), residues: 288 loop : -1.86 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.024 0.001 TYR S 178 PHE 0.024 0.001 PHE S 68 TRP 0.029 0.002 TRP S 111 HIS 0.010 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9771) covalent geometry : angle 0.62443 (13248) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.86732 ( 12) hydrogen bonds : bond 0.02777 ( 358) hydrogen bonds : angle 4.28928 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7409 (mtm110) REVERT: A 277 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7748 (ttmt) REVERT: A 304 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 15 LYS cc_start: 0.8973 (tptt) cc_final: 0.8547 (ttmm) REVERT: B 61 MET cc_start: 0.8683 (ppp) cc_final: 0.8115 (ppp) REVERT: B 129 ARG cc_start: 0.7882 (tpp-160) cc_final: 0.7514 (mmm160) REVERT: B 134 ARG cc_start: 0.8681 (ptt-90) cc_final: 0.8324 (ptt-90) REVERT: B 210 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9086 (tp) REVERT: B 211 TRP cc_start: 0.9152 (m100) cc_final: 0.8899 (m100) REVERT: B 275 SER cc_start: 0.8782 (m) cc_final: 0.8577 (m) REVERT: B 292 PHE cc_start: 0.7956 (m-80) cc_final: 0.7429 (m-80) REVERT: B 297 TRP cc_start: 0.8877 (m100) cc_final: 0.8650 (m100) REVERT: B 325 MET cc_start: 0.8809 (tpp) cc_final: 0.8549 (tpp) REVERT: R 63 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7381 (mm) REVERT: R 126 LYS cc_start: 0.6914 (ttmm) cc_final: 0.6560 (tppt) REVERT: R 209 MET cc_start: 0.7668 (mmm) cc_final: 0.7269 (mmm) REVERT: R 216 GLN cc_start: 0.7960 (tp40) cc_final: 0.7319 (tm-30) REVERT: R 226 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8822 (tt) REVERT: R 293 ASP cc_start: 0.9076 (t0) cc_final: 0.8778 (t0) REVERT: S 3 GLN cc_start: 0.7888 (pt0) cc_final: 0.7635 (pt0) REVERT: S 29 PHE cc_start: 0.8969 (t80) cc_final: 0.8768 (t80) REVERT: S 86 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8840 (pp) REVERT: S 91 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7963 (t) REVERT: S 219 GLN cc_start: 0.9049 (pp30) cc_final: 0.8704 (pp30) outliers start: 45 outliers final: 35 residues processed: 268 average time/residue: 0.1003 time to fit residues: 37.4309 Evaluate side-chains 260 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS C 18 GLN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120537 restraints weight = 14322.344| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.86 r_work: 0.3429 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9777 Z= 0.124 Angle : 0.641 10.571 13260 Z= 0.318 Chirality : 0.043 0.251 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.739 33.746 1392 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.09 % Allowed : 25.00 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1212 helix: 0.07 (0.27), residues: 401 sheet: -1.62 (0.30), residues: 288 loop : -1.76 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.025 0.001 TYR S 178 PHE 0.011 0.001 PHE R 97 TRP 0.035 0.002 TRP S 111 HIS 0.017 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9771) covalent geometry : angle 0.64055 (13248) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.90676 ( 12) hydrogen bonds : bond 0.02849 ( 358) hydrogen bonds : angle 4.30115 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7279 (mtm110) REVERT: A 277 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7803 (ttmt) REVERT: A 304 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 15 LYS cc_start: 0.9001 (tptt) cc_final: 0.8555 (ttmm) REVERT: B 61 MET cc_start: 0.8744 (ppp) cc_final: 0.8172 (ppp) REVERT: B 124 TYR cc_start: 0.9013 (m-80) cc_final: 0.8765 (m-10) REVERT: B 129 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7541 (mmm160) REVERT: B 134 ARG cc_start: 0.8733 (ptt-90) cc_final: 0.8360 (ptt-90) REVERT: B 172 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: B 210 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 211 TRP cc_start: 0.9147 (m100) cc_final: 0.8871 (m100) REVERT: B 215 GLU cc_start: 0.8737 (mp0) cc_final: 0.8125 (pm20) REVERT: B 275 SER cc_start: 0.8952 (m) cc_final: 0.8745 (m) REVERT: B 292 PHE cc_start: 0.8052 (m-80) cc_final: 0.7444 (m-80) REVERT: B 297 TRP cc_start: 0.8914 (m100) cc_final: 0.8706 (m100) REVERT: B 325 MET cc_start: 0.8890 (tpp) cc_final: 0.8598 (tpp) REVERT: R 63 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7377 (mm) REVERT: R 90 LEU cc_start: 0.7991 (tp) cc_final: 0.7550 (tt) REVERT: R 126 LYS cc_start: 0.6876 (ttmm) cc_final: 0.6511 (tppt) REVERT: R 183 PHE cc_start: 0.8647 (m-80) cc_final: 0.8140 (m-80) REVERT: R 209 MET cc_start: 0.7642 (mmm) cc_final: 0.7212 (mmm) REVERT: R 216 GLN cc_start: 0.7962 (tp40) cc_final: 0.7290 (tm-30) REVERT: R 226 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8780 (tt) REVERT: R 293 ASP cc_start: 0.9094 (t0) cc_final: 0.8801 (t0) REVERT: S 3 GLN cc_start: 0.7966 (pt0) cc_final: 0.7718 (pt0) REVERT: S 29 PHE cc_start: 0.9038 (t80) cc_final: 0.8787 (t80) REVERT: S 86 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8849 (pp) REVERT: S 91 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7974 (t) REVERT: S 219 GLN cc_start: 0.9130 (pp30) cc_final: 0.8737 (pp30) outliers start: 42 outliers final: 35 residues processed: 254 average time/residue: 0.0959 time to fit residues: 33.8019 Evaluate side-chains 262 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121997 restraints weight = 14274.862| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.77 r_work: 0.3460 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9777 Z= 0.118 Angle : 0.649 10.411 13260 Z= 0.321 Chirality : 0.043 0.245 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.689 33.924 1392 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.18 % Allowed : 25.10 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1212 helix: 0.18 (0.27), residues: 401 sheet: -1.56 (0.30), residues: 287 loop : -1.70 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.013 0.001 TYR A 296 PHE 0.015 0.001 PHE S 68 TRP 0.036 0.002 TRP S 111 HIS 0.021 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9771) covalent geometry : angle 0.64877 (13248) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.89723 ( 12) hydrogen bonds : bond 0.02785 ( 358) hydrogen bonds : angle 4.26735 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7234 (mtm110) REVERT: A 277 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7840 (ttmt) REVERT: A 304 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 15 LYS cc_start: 0.8996 (tptt) cc_final: 0.8549 (ttmm) REVERT: B 61 MET cc_start: 0.8757 (ppp) cc_final: 0.8167 (ppp) REVERT: B 124 TYR cc_start: 0.9040 (m-80) cc_final: 0.8742 (m-10) REVERT: B 129 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7515 (mmm160) REVERT: B 134 ARG cc_start: 0.8718 (ptt-90) cc_final: 0.8330 (ptt-90) REVERT: B 210 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B 211 TRP cc_start: 0.9106 (m100) cc_final: 0.8857 (m100) REVERT: B 275 SER cc_start: 0.8851 (m) cc_final: 0.8610 (m) REVERT: B 325 MET cc_start: 0.8884 (tpp) cc_final: 0.8580 (tpp) REVERT: C 18 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8145 (tp40) REVERT: C 22 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7207 (tp30) REVERT: R 63 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7347 (mm) REVERT: R 90 LEU cc_start: 0.8071 (tp) cc_final: 0.7613 (tt) REVERT: R 126 LYS cc_start: 0.6791 (ttmm) cc_final: 0.6391 (tppt) REVERT: R 209 MET cc_start: 0.7833 (mmm) cc_final: 0.7276 (mmm) REVERT: R 216 GLN cc_start: 0.7944 (tp40) cc_final: 0.7282 (tm-30) REVERT: R 226 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8689 (tt) REVERT: R 293 ASP cc_start: 0.9091 (t0) cc_final: 0.8793 (t0) REVERT: S 3 GLN cc_start: 0.8075 (pt0) cc_final: 0.7818 (pt0) REVERT: S 29 PHE cc_start: 0.9023 (t80) cc_final: 0.8804 (t80) REVERT: S 86 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8834 (pp) REVERT: S 91 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7976 (t) REVERT: S 219 GLN cc_start: 0.9142 (pp30) cc_final: 0.8694 (pp30) outliers start: 43 outliers final: 34 residues processed: 261 average time/residue: 0.0920 time to fit residues: 33.8283 Evaluate side-chains 259 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN S 39 GLN ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122429 restraints weight = 14473.183| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.74 r_work: 0.3480 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9777 Z= 0.151 Angle : 0.676 10.915 13260 Z= 0.333 Chirality : 0.043 0.242 1531 Planarity : 0.004 0.084 1660 Dihedral : 4.833 34.462 1392 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.38 % Allowed : 24.90 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.24), residues: 1212 helix: 0.20 (0.27), residues: 402 sheet: -1.61 (0.30), residues: 290 loop : -1.64 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 8 TYR 0.012 0.001 TYR S 215 PHE 0.035 0.001 PHE S 68 TRP 0.040 0.002 TRP S 111 HIS 0.017 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9771) covalent geometry : angle 0.67573 (13248) SS BOND : bond 0.00156 ( 6) SS BOND : angle 1.07677 ( 12) hydrogen bonds : bond 0.02882 ( 358) hydrogen bonds : angle 4.31804 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.45 seconds wall clock time: 41 minutes 32.93 seconds (2492.93 seconds total)