Starting phenix.real_space_refine on Fri Sep 11 19:31:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lfo_0879/09_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_0879/09_2026/6lfo_0879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lfo_0879/09_2026/6lfo_0879.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.18, 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: 0.77 Conformation dependent library (CDL) restraints added in 365.7 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: 0.30 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: 1.42 Time building geometry restraints manager: 1.00 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: 5119 17.97 - 35.93: 591 35.93 - 53.90: 86 53.90 - 71.86: 15 71.86 - 89.83: 8 Dihedral angle restraints: 5819 sinusoidal: 2253 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 5816 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.790 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 15.028 89.828 3497 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/Z covalent geometry : bond 0.01281 / 0.57 ( 9771) covalent geometry : angle 1.13316 / 0.59 (13248) SS BOND : bond 0.01034 / 0.54 ( 6) SS BOND : angle 1.68996 / 0.94 ( 12) hydrogen bonds : bond 0.29978 / 19.65 ( 358) hydrogen bonds : angle 10.83373 / 7.39 ( 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 : 0.381 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: 0.1106 time to fit residues: 45.2253 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 : 0.360 ------------------------------------------------------------------------------- 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... A 204 GLN A 213 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.156322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119720 restraints weight = 14461.229| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.84 r_work: 0.3415 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2458 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= 0.142 Angle : 0.660 8.511 13260 Z= 0.341 Chirality : 0.043 0.162 1531 Planarity : 0.005 0.091 1660 Dihedral : 5.716 37.827 1339 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.02 % Allowed : 18.29 % Favored : 78.70 % 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: -4.28 (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 0.011 0.001 PHE A 334 TRP 0.023 0.001 TRP R 112 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9771) covalent geometry : angle 0.65790 / 0.34 (13248) SS BOND : bond 0.00288 / 0.13 ( 6) SS BOND : angle 1.68414 / 0.93 ( 12) hydrogen bonds : bond 0.04244 / 2.74 ( 358) hydrogen bonds : angle 5.82829 / 3.97 ( 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 317 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.373 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: 0.8026 (mtt-85) cc_final: 0.7578 (mtm110) REVERT: A 304 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 310 LEU cc_start: 0.8915 (mt) cc_final: 0.8529 (mt) REVERT: B 9 GLN cc_start: 0.8278 (mm110) cc_final: 0.7957 (mp10) REVERT: B 15 LYS cc_start: 0.9106 (tptt) cc_final: 0.8794 (mtpp) REVERT: B 17 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 129 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7574 (mmm160) REVERT: B 292 PHE cc_start: 0.8029 (m-10) cc_final: 0.7626 (m-80) REVERT: C 38 MET cc_start: 0.8862 (ttp) cc_final: 0.8638 (ttp) REVERT: C 47 GLU cc_start: 0.7836 (mp0) cc_final: 0.7288 (mp0) REVERT: D 39 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6421 (tp) REVERT: R 63 LEU cc_start: 0.7877 (mm) cc_final: 0.7452 (mm) REVERT: R 95 LEU cc_start: 0.8615 (tp) cc_final: 0.8222 (pp) REVERT: R 134 ILE cc_start: 0.8475 (mm) cc_final: 0.8273 (mm) REVERT: R 173 SER cc_start: 0.9142 (t) cc_final: 0.8926 (p) REVERT: R 209 MET cc_start: 0.7621 (mmm) cc_final: 0.7096 (mmm) REVERT: R 226 ILE cc_start: 0.9216 (tt) cc_final: 0.8878 (tt) REVERT: R 242 HIS cc_start: 0.7811 (p90) cc_final: 0.7542 (p-80) REVERT: S 3 GLN cc_start: 0.8186 (pt0) cc_final: 0.7916 (pt0) REVERT: S 20 LEU cc_start: 0.7712 (mt) cc_final: 0.7420 (mt) REVERT: S 219 GLN cc_start: 0.9098 (pp30) cc_final: 0.8653 (pp30) REVERT: S 232 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7931 (ttpp) outliers start: 31 outliers final: 13 residues processed: 302 average time/residue: 0.0889 time to fit residues: 37.0030 Evaluate side-chains 247 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 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: 2.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS B 295 ASN D 8 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110257 restraints weight = 14472.875| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.64 r_work: 0.3302 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9777 Z= 0.324 Angle : 0.775 9.239 13260 Z= 0.396 Chirality : 0.047 0.243 1531 Planarity : 0.005 0.091 1660 Dihedral : 5.878 37.382 1336 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.54 % Allowed : 20.72 % Favored : 73.74 % 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: -3.51 (0.22), residues: 1212 helix: -1.73 (0.23), residues: 399 sheet: -2.72 (0.28), residues: 276 loop : -2.46 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 27 TYR 0.035 0.002 TYR S 178 PHE 0.017 0.002 PHE A 307 TRP 0.028 0.002 TRP R 112 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.32 ( 9771) covalent geometry : angle 0.77450 / 0.40 (13248) SS BOND : bond 0.00530 / 0.26 ( 6) SS BOND : angle 1.45816 / 0.80 ( 12) hydrogen bonds : bond 0.03926 / 2.56 ( 358) hydrogen bonds : angle 5.34831 / 3.69 ( 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 293 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.7864 (mtm110) REVERT: A 243 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: A 277 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7794 (ttmt) REVERT: A 310 LEU cc_start: 0.9255 (mt) cc_final: 0.8595 (mt) REVERT: A 341 ASP cc_start: 0.8935 (t70) cc_final: 0.8692 (t0) REVERT: B 15 LYS cc_start: 0.9108 (tptt) cc_final: 0.8575 (ttmm) REVERT: B 17 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 129 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7672 (mmm160) REVERT: B 188 MET cc_start: 0.9209 (mmm) cc_final: 0.8534 (tpp) REVERT: B 209 LYS cc_start: 0.9170 (mttm) cc_final: 0.8848 (mttt) REVERT: B 210 LEU cc_start: 0.9476 (tp) cc_final: 0.9240 (tp) REVERT: B 292 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: B 295 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: B 322 ASP cc_start: 0.8822 (m-30) cc_final: 0.8426 (t0) REVERT: B 325 MET cc_start: 0.9006 (tpp) cc_final: 0.8681 (tpp) REVERT: C 38 MET cc_start: 0.9146 (ttp) cc_final: 0.8938 (ttp) REVERT: C 47 GLU cc_start: 0.8108 (mp0) cc_final: 0.7515 (mp0) REVERT: C 55 PRO cc_start: 0.7928 (Cg_exo) cc_final: 0.7593 (Cg_endo) REVERT: D 39 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6323 (tp) REVERT: R 63 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7647 (mm) REVERT: R 99 LEU cc_start: 0.8652 (mm) cc_final: 0.8380 (mm) REVERT: R 126 LYS cc_start: 0.7563 (ttmm) cc_final: 0.6671 (ttpt) REVERT: R 134 ILE cc_start: 0.8665 (mm) cc_final: 0.8432 (mm) REVERT: R 209 MET cc_start: 0.8000 (mmm) cc_final: 0.7505 (mmm) REVERT: R 226 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8891 (tt) REVERT: R 242 HIS cc_start: 0.7877 (p90) cc_final: 0.7360 (p-80) REVERT: S 3 GLN cc_start: 0.8572 (pt0) cc_final: 0.8367 (pt0) REVERT: S 47 TRP cc_start: 0.8621 (t60) cc_final: 0.8307 (t60) REVERT: S 91 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8198 (t) REVERT: S 219 GLN cc_start: 0.9290 (pp30) cc_final: 0.8887 (pp30) outliers start: 57 outliers final: 32 residues processed: 277 average time/residue: 0.0972 time to fit residues: 38.1199 Evaluate side-chains 254 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL 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 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 180 VAL 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 305 LEU 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 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 198 THR 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 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 245 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 = 0.4060 r_free = 0.4060 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122119 restraints weight = 14899.788| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.20 r_work: 0.3420 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9777 Z= 0.130 Angle : 0.629 8.858 13260 Z= 0.317 Chirality : 0.042 0.158 1531 Planarity : 0.004 0.088 1660 Dihedral : 5.286 37.015 1336 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.09 % Allowed : 23.15 % Favored : 72.76 % 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: -3.00 (0.23), residues: 1212 helix: -1.23 (0.24), residues: 408 sheet: -2.37 (0.29), residues: 285 loop : -2.25 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.021 0.001 TYR S 178 PHE 0.013 0.001 PHE R 97 TRP 0.022 0.001 TRP R 112 HIS 0.005 0.001 HIS R 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9771) covalent geometry : angle 0.62828 / 0.32 (13248) SS BOND : bond 0.00230 / 0.10 ( 6) SS BOND : angle 1.01921 / 0.56 ( 12) hydrogen bonds : bond 0.03184 / 2.07 ( 358) hydrogen bonds : angle 4.78699 / 3.29 ( 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 298 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7713 (mtm110) REVERT: A 240 MET cc_start: 0.7550 (tpp) cc_final: 0.6946 (ptp) REVERT: A 243 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: A 277 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7801 (ttmt) REVERT: A 304 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 310 LEU cc_start: 0.9184 (mt) cc_final: 0.8700 (mt) REVERT: B 9 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7616 (mp10) REVERT: B 15 LYS cc_start: 0.9016 (tptt) cc_final: 0.8566 (ttmm) REVERT: B 17 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 129 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.7711 (mmm160) REVERT: B 188 MET cc_start: 0.9054 (mmm) cc_final: 0.8356 (tpp) REVERT: B 210 LEU cc_start: 0.9475 (tp) cc_final: 0.9236 (tp) REVERT: B 215 GLU cc_start: 0.8742 (mp0) cc_final: 0.8541 (mp0) REVERT: B 258 ASP cc_start: 0.7458 (t0) cc_final: 0.7203 (t0) REVERT: B 292 PHE cc_start: 0.8242 (m-10) cc_final: 0.7887 (m-80) REVERT: B 325 MET cc_start: 0.8820 (tpp) cc_final: 0.8515 (tpp) REVERT: C 13 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8491 (ptp-170) REVERT: C 47 GLU cc_start: 0.7999 (mp0) cc_final: 0.7517 (mp0) REVERT: C 58 GLU cc_start: 0.8673 (pt0) cc_final: 0.7961 (pm20) REVERT: D 39 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.6225 (tp) REVERT: R 63 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7483 (mm) REVERT: R 95 LEU cc_start: 0.8553 (tp) cc_final: 0.8034 (pp) REVERT: R 126 LYS cc_start: 0.7668 (ttmm) cc_final: 0.6944 (ttpt) REVERT: R 134 ILE cc_start: 0.8402 (mm) cc_final: 0.8163 (mm) REVERT: R 209 MET cc_start: 0.7829 (mmm) cc_final: 0.7397 (mmm) REVERT: R 216 GLN cc_start: 0.8011 (tp40) cc_final: 0.7165 (tm-30) REVERT: R 226 ILE cc_start: 0.9221 (tt) cc_final: 0.8868 (tt) REVERT: S 3 GLN cc_start: 0.8204 (pt0) cc_final: 0.8000 (pt0) REVERT: S 47 TRP cc_start: 0.8354 (t60) cc_final: 0.8138 (t60) REVERT: S 86 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8856 (pp) REVERT: S 91 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8062 (t) REVERT: S 171 GLN cc_start: 0.8179 (pt0) cc_final: 0.7925 (pp30) REVERT: S 219 GLN cc_start: 0.9137 (pp30) cc_final: 0.8765 (pp30) outliers start: 42 outliers final: 24 residues processed: 283 average time/residue: 0.1041 time to fit residues: 41.4378 Evaluate side-chains 265 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 61 MET 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 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP 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 119 CYS Chi-restraints excluded: chain R residue 124 LEU 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 77 ASN 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 100 ILE Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119091 restraints weight = 14398.199| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.79 r_work: 0.3404 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9777 Z= 0.118 Angle : 0.612 8.853 13260 Z= 0.306 Chirality : 0.042 0.147 1531 Planarity : 0.004 0.088 1660 Dihedral : 4.962 35.141 1336 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.77 % Allowed : 22.47 % Favored : 72.76 % 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: -2.61 (0.23), residues: 1212 helix: -0.83 (0.25), residues: 410 sheet: -2.13 (0.29), residues: 289 loop : -2.11 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.022 0.001 TYR S 178 PHE 0.016 0.001 PHE R 97 TRP 0.018 0.001 TRP R 112 HIS 0.005 0.001 HIS R 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9771) covalent geometry : angle 0.61139 / 0.31 (13248) SS BOND : bond 0.00352 / 0.18 ( 6) SS BOND : angle 1.05298 / 0.58 ( 12) hydrogen bonds : bond 0.02972 / 1.95 ( 358) hydrogen bonds : angle 4.51842 / 3.09 ( 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 302 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.7631 (mtm110) REVERT: A 240 MET cc_start: 0.7565 (tpp) cc_final: 0.7039 (ptt) REVERT: A 243 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8247 (mmm) REVERT: A 277 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7785 (ttmt) REVERT: A 304 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 310 LEU cc_start: 0.9226 (mt) cc_final: 0.8634 (mt) REVERT: B 9 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7793 (mp10) REVERT: B 15 LYS cc_start: 0.9010 (tptt) cc_final: 0.8546 (ttmm) REVERT: B 17 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 129 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7584 (mmm160) REVERT: B 188 MET cc_start: 0.8950 (mmm) cc_final: 0.8443 (tpp) REVERT: B 210 LEU cc_start: 0.9351 (tp) cc_final: 0.9117 (tp) REVERT: B 275 SER cc_start: 0.8791 (m) cc_final: 0.8537 (m) REVERT: B 292 PHE cc_start: 0.8181 (m-10) cc_final: 0.7630 (m-80) REVERT: B 297 TRP cc_start: 0.8936 (m100) cc_final: 0.8695 (m100) REVERT: B 325 MET cc_start: 0.8820 (tpp) cc_final: 0.8502 (tpp) REVERT: C 22 GLU cc_start: 0.7579 (tp30) cc_final: 0.7323 (tp30) REVERT: C 27 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7331 (mtt90) REVERT: C 58 GLU cc_start: 0.8554 (pt0) cc_final: 0.7805 (pm20) REVERT: R 63 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7434 (mm) REVERT: R 95 LEU cc_start: 0.8533 (tp) cc_final: 0.8094 (pp) REVERT: R 126 LYS cc_start: 0.7376 (ttmm) cc_final: 0.6822 (ttpt) REVERT: R 209 MET cc_start: 0.7704 (mmm) cc_final: 0.7309 (mmm) REVERT: R 216 GLN cc_start: 0.7845 (tp40) cc_final: 0.7174 (tm-30) REVERT: R 226 ILE cc_start: 0.9130 (tt) cc_final: 0.8762 (tt) REVERT: R 293 ASP cc_start: 0.9039 (t0) cc_final: 0.8797 (t0) REVERT: S 3 GLN cc_start: 0.8200 (pt0) cc_final: 0.7956 (pt0) REVERT: S 47 TRP cc_start: 0.8388 (t60) cc_final: 0.8155 (t60) REVERT: S 86 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8866 (pp) REVERT: S 91 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8011 (t) REVERT: S 171 GLN cc_start: 0.8040 (pt0) cc_final: 0.7838 (pp30) REVERT: S 219 GLN cc_start: 0.9206 (pp30) cc_final: 0.8744 (pp30) outliers start: 49 outliers final: 31 residues processed: 287 average time/residue: 0.1028 time to fit residues: 41.1750 Evaluate side-chains 265 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 61 MET 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 89 ASN ** 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 = 0.4015 r_free = 0.4015 target = 0.156726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118685 restraints weight = 14278.838| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.73 r_work: 0.3410 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9777 Z= 0.123 Angle : 0.625 8.867 13260 Z= 0.314 Chirality : 0.042 0.161 1531 Planarity : 0.004 0.087 1660 Dihedral : 4.896 34.689 1336 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.16 % Allowed : 22.76 % Favored : 72.08 % 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: -2.35 (0.23), residues: 1212 helix: -0.54 (0.26), residues: 404 sheet: -2.02 (0.29), residues: 292 loop : -1.99 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.023 0.001 TYR S 178 PHE 0.015 0.001 PHE R 97 TRP 0.042 0.002 TRP R 112 HIS 0.004 0.001 HIS R 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9771) covalent geometry : angle 0.62470 / 0.31 (13248) SS BOND : bond 0.00155 / 0.06 ( 6) SS BOND : angle 1.03236 / 0.57 ( 12) hydrogen bonds : bond 0.02927 / 1.90 ( 358) hydrogen bonds : angle 4.45371 / 3.05 ( 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 297 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7670 (mtm110) REVERT: A 216 GLU cc_start: 0.8245 (tt0) cc_final: 0.7923 (tt0) REVERT: A 240 MET cc_start: 0.7529 (tpp) cc_final: 0.7114 (ptt) REVERT: A 243 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: A 277 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7839 (ttmt) REVERT: A 304 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 310 LEU cc_start: 0.9214 (mt) cc_final: 0.8616 (mt) REVERT: B 9 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7835 (mp10) REVERT: B 15 LYS cc_start: 0.9076 (tptt) cc_final: 0.8586 (ttmm) REVERT: B 17 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 129 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7552 (mmm160) REVERT: B 210 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9076 (tp) REVERT: B 275 SER cc_start: 0.8769 (m) cc_final: 0.8531 (m) REVERT: B 292 PHE cc_start: 0.8159 (m-10) cc_final: 0.7587 (m-80) REVERT: B 325 MET cc_start: 0.8850 (tpp) cc_final: 0.8602 (tpp) REVERT: C 58 GLU cc_start: 0.8454 (pt0) cc_final: 0.7695 (pm20) REVERT: R 63 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7426 (mm) REVERT: R 80 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7496 (mmp80) REVERT: R 126 LYS cc_start: 0.7289 (ttmm) cc_final: 0.6799 (ttpt) REVERT: R 209 MET cc_start: 0.7684 (mmm) cc_final: 0.7289 (mmm) REVERT: R 216 GLN cc_start: 0.7727 (tp40) cc_final: 0.7158 (tm-30) REVERT: R 226 ILE cc_start: 0.9120 (tt) cc_final: 0.8770 (tt) REVERT: R 293 ASP cc_start: 0.9054 (t0) cc_final: 0.8813 (t0) REVERT: S 3 GLN cc_start: 0.8128 (pt0) cc_final: 0.7913 (pt0) REVERT: S 47 TRP cc_start: 0.8380 (t60) cc_final: 0.8169 (t60) REVERT: S 86 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8876 (pp) REVERT: S 91 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (t) REVERT: S 219 GLN cc_start: 0.9176 (pp30) cc_final: 0.8734 (pp30) outliers start: 53 outliers final: 37 residues processed: 280 average time/residue: 0.1028 time to fit residues: 40.2929 Evaluate side-chains 272 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 224 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 61 MET 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 210 LEU Chi-restraints excluded: chain B residue 220 GLN 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 C residue 54 VAL 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 123 SER 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 100 ILE 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 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: 0.1980 chunk 105 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** 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 = 0.4017 r_free = 0.4017 target = 0.157160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118431 restraints weight = 14415.619| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.75 r_work: 0.3392 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4033 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 : 0.631 9.476 13260 Z= 0.316 Chirality : 0.043 0.159 1531 Planarity : 0.004 0.087 1660 Dihedral : 4.928 33.994 1336 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.16 % Allowed : 23.35 % Favored : 71.50 % 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: -2.19 (0.24), residues: 1212 helix: -0.44 (0.26), residues: 410 sheet: -1.93 (0.29), residues: 292 loop : -1.88 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.025 0.001 TYR S 178 PHE 0.015 0.001 PHE R 97 TRP 0.035 0.002 TRP R 112 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9771) covalent geometry : angle 0.63086 / 0.32 (13248) SS BOND : bond 0.00163 / 0.07 ( 6) SS BOND : angle 0.92048 / 0.51 ( 12) hydrogen bonds : bond 0.02895 / 1.89 ( 358) hydrogen bonds : angle 4.44352 / 3.05 ( 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 296 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7393 (mtm110) REVERT: A 277 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7860 (ttmt) REVERT: A 304 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 310 LEU cc_start: 0.9221 (mt) cc_final: 0.8580 (mt) REVERT: B 15 LYS cc_start: 0.9079 (tptt) cc_final: 0.8563 (ttmm) REVERT: B 17 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 129 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7549 (mmm160) REVERT: B 210 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9098 (tp) REVERT: B 275 SER cc_start: 0.8793 (m) cc_final: 0.8566 (m) REVERT: B 292 PHE cc_start: 0.8279 (m-10) cc_final: 0.7724 (m-80) REVERT: B 325 MET cc_start: 0.8908 (tpp) cc_final: 0.8670 (tpp) REVERT: C 13 ARG cc_start: 0.8850 (ptm160) cc_final: 0.8614 (ptm160) REVERT: C 22 GLU cc_start: 0.7638 (tp30) cc_final: 0.7168 (tp30) REVERT: C 58 GLU cc_start: 0.8492 (pt0) cc_final: 0.7692 (pm20) REVERT: D 59 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7082 (mm110) REVERT: R 63 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7450 (mm) REVERT: R 80 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7358 (mmp80) REVERT: R 126 LYS cc_start: 0.7377 (ttmm) cc_final: 0.6842 (ttpt) REVERT: R 209 MET cc_start: 0.7707 (mmm) cc_final: 0.7284 (mmm) REVERT: R 216 GLN cc_start: 0.7719 (tp40) cc_final: 0.7099 (pp30) REVERT: R 226 ILE cc_start: 0.9112 (tt) cc_final: 0.8760 (tt) REVERT: R 293 ASP cc_start: 0.9181 (t0) cc_final: 0.8927 (t0) REVERT: S 3 GLN cc_start: 0.8150 (pt0) cc_final: 0.7925 (pt0) REVERT: S 20 LEU cc_start: 0.7756 (mm) cc_final: 0.7514 (mp) REVERT: S 47 TRP cc_start: 0.8452 (t60) cc_final: 0.8237 (t60) REVERT: S 86 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8878 (pp) REVERT: S 91 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7968 (t) REVERT: S 219 GLN cc_start: 0.9184 (pp30) cc_final: 0.8740 (pp30) outliers start: 53 outliers final: 39 residues processed: 275 average time/residue: 0.1048 time to fit residues: 40.1638 Evaluate side-chains 275 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 224 CYS 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 210 LEU Chi-restraints excluded: chain B residue 220 GLN 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 C residue 54 VAL 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 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 180 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 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL 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 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS R 319 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 = 0.4014 r_free = 0.4014 target = 0.156786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118366 restraints weight = 14485.609| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.78 r_work: 0.3410 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4226 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= 0.126 Angle : 0.642 9.548 13260 Z= 0.321 Chirality : 0.043 0.281 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.850 34.212 1336 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.57 % Allowed : 24.71 % 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: -2.02 (0.24), residues: 1212 helix: -0.27 (0.26), residues: 408 sheet: -1.82 (0.30), residues: 291 loop : -1.82 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.024 0.001 TYR S 178 PHE 0.020 0.001 PHE S 68 TRP 0.030 0.002 TRP S 111 HIS 0.006 0.001 HIS R 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9771) covalent geometry : angle 0.64149 / 0.32 (13248) SS BOND : bond 0.00182 / 0.10 ( 6) SS BOND : angle 0.91793 / 0.51 ( 12) hydrogen bonds : bond 0.02827 / 1.84 ( 358) hydrogen bonds : angle 4.37965 / 3.00 ( 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 280 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.374 Fit side-chains REVERT: A 32 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7374 (mtm110) REVERT: A 240 MET cc_start: 0.7145 (tpp) cc_final: 0.6812 (ptt) REVERT: A 277 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7898 (ttmt) REVERT: A 304 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 310 LEU cc_start: 0.9205 (mt) cc_final: 0.8609 (mt) REVERT: B 15 LYS cc_start: 0.9064 (tptt) cc_final: 0.8599 (ttmm) REVERT: B 129 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7537 (mmm160) REVERT: B 210 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9106 (tp) REVERT: B 215 GLU cc_start: 0.8861 (mp0) cc_final: 0.8136 (pm20) REVERT: B 275 SER cc_start: 0.8770 (m) cc_final: 0.8533 (m) REVERT: B 292 PHE cc_start: 0.8111 (m-10) cc_final: 0.7547 (m-80) REVERT: B 325 MET cc_start: 0.8875 (tpp) cc_final: 0.8657 (tpp) REVERT: C 13 ARG cc_start: 0.8848 (ptm160) cc_final: 0.8648 (ptm160) REVERT: C 22 GLU cc_start: 0.7480 (tp30) cc_final: 0.7184 (tp30) REVERT: D 59 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7065 (mm110) REVERT: R 63 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7391 (mm) REVERT: R 80 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7387 (mmp80) REVERT: R 209 MET cc_start: 0.7680 (mmm) cc_final: 0.7244 (mmm) REVERT: R 216 GLN cc_start: 0.8015 (tp40) cc_final: 0.7326 (tm-30) REVERT: R 226 ILE cc_start: 0.9111 (tt) cc_final: 0.8753 (tt) REVERT: R 293 ASP cc_start: 0.9140 (t0) cc_final: 0.8878 (t0) REVERT: S 3 GLN cc_start: 0.8120 (pt0) cc_final: 0.7906 (pt0) REVERT: S 20 LEU cc_start: 0.7731 (mm) cc_final: 0.7473 (mp) REVERT: S 47 TRP cc_start: 0.8376 (t60) cc_final: 0.8160 (t60) REVERT: S 86 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8890 (pp) REVERT: S 91 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7942 (t) REVERT: S 219 GLN cc_start: 0.9160 (pp30) cc_final: 0.8740 (pp30) outliers start: 47 outliers final: 39 residues processed: 265 average time/residue: 0.1040 time to fit residues: 38.3396 Evaluate side-chains 264 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS 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 210 LEU Chi-restraints excluded: chain B residue 223 THR 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 C residue 54 VAL 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 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 229 PHE 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 R residue 327 LYS 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 Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 89 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 = 0.4038 r_free = 0.4038 target = 0.159234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120766 restraints weight = 14454.703| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.77 r_work: 0.3429 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9777 Z= 0.122 Angle : 0.637 9.703 13260 Z= 0.317 Chirality : 0.043 0.262 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.808 33.711 1336 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.67 % Allowed : 24.71 % Favored : 70.62 % 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: -1.82 (0.24), residues: 1212 helix: -0.08 (0.26), residues: 406 sheet: -1.71 (0.30), residues: 291 loop : -1.72 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.024 0.001 TYR S 178 PHE 0.015 0.001 PHE R 97 TRP 0.033 0.002 TRP S 111 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9771) covalent geometry : angle 0.63613 / 0.32 (13248) SS BOND : bond 0.00284 / 0.14 ( 6) SS BOND : angle 1.18650 / 0.65 ( 12) hydrogen bonds : bond 0.02804 / 1.82 ( 358) hydrogen bonds : angle 4.35723 / 2.98 ( 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 278 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7365 (mtm110) REVERT: A 240 MET cc_start: 0.7295 (tpp) cc_final: 0.6857 (ptt) REVERT: A 277 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7924 (ttmt) REVERT: A 304 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 310 LEU cc_start: 0.9194 (mt) cc_final: 0.8612 (mt) REVERT: B 15 LYS cc_start: 0.9055 (tptt) cc_final: 0.8582 (ttmm) REVERT: B 129 ARG cc_start: 0.7874 (tpp-160) cc_final: 0.7511 (mmm160) REVERT: B 172 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: B 210 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9078 (tp) REVERT: B 275 SER cc_start: 0.8752 (m) cc_final: 0.8516 (m) REVERT: B 292 PHE cc_start: 0.8083 (m-10) cc_final: 0.7487 (m-80) REVERT: B 325 MET cc_start: 0.8903 (tpp) cc_final: 0.8635 (tpp) REVERT: C 13 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8717 (ptm160) REVERT: C 22 GLU cc_start: 0.7372 (tp30) cc_final: 0.7049 (tp30) REVERT: D 59 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7003 (mm110) REVERT: R 63 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7455 (mm) REVERT: R 80 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7212 (mmp80) REVERT: R 104 TRP cc_start: 0.7367 (t-100) cc_final: 0.6780 (t-100) REVERT: R 209 MET cc_start: 0.7650 (mmm) cc_final: 0.7238 (mmm) REVERT: R 216 GLN cc_start: 0.7971 (tp40) cc_final: 0.7260 (tm-30) REVERT: R 226 ILE cc_start: 0.9187 (tt) cc_final: 0.8832 (tt) REVERT: R 293 ASP cc_start: 0.9159 (t0) cc_final: 0.8899 (t0) REVERT: R 319 GLN cc_start: 0.7241 (tp40) cc_final: 0.6958 (tp-100) REVERT: S 3 GLN cc_start: 0.8096 (pt0) cc_final: 0.7888 (pt0) REVERT: S 20 LEU cc_start: 0.7682 (mm) cc_final: 0.7469 (mp) REVERT: S 47 TRP cc_start: 0.8345 (t60) cc_final: 0.8142 (t60) REVERT: S 86 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8880 (pp) REVERT: S 91 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7938 (t) REVERT: S 219 GLN cc_start: 0.9169 (pp30) cc_final: 0.8725 (pp30) outliers start: 48 outliers final: 40 residues processed: 262 average time/residue: 0.1013 time to fit residues: 36.9489 Evaluate side-chains 270 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS 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 160 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 54 VAL 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 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 R residue 327 LYS 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 Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.163215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124754 restraints weight = 14566.595| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.87 r_work: 0.3512 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9777 Z= 0.122 Angle : 0.660 10.165 13260 Z= 0.328 Chirality : 0.043 0.260 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.782 32.776 1336 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.77 % Allowed : 25.19 % Favored : 70.04 % 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: -1.67 (0.24), residues: 1212 helix: 0.14 (0.27), residues: 399 sheet: -1.68 (0.30), residues: 291 loop : -1.66 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.012 0.001 TYR S 178 PHE 0.020 0.001 PHE S 68 TRP 0.035 0.002 TRP S 111 HIS 0.017 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9771) covalent geometry : angle 0.65947 / 0.33 (13248) SS BOND : bond 0.00198 / 0.10 ( 6) SS BOND : angle 0.80698 / 0.44 ( 12) hydrogen bonds : bond 0.02796 / 1.82 ( 358) hydrogen bonds : angle 4.38095 / 3.02 ( 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 284 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7171 (mtm110) REVERT: A 277 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7773 (ttmt) REVERT: A 304 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 310 LEU cc_start: 0.9148 (mt) cc_final: 0.8590 (mt) REVERT: B 15 LYS cc_start: 0.9051 (tptt) cc_final: 0.8577 (ttmm) REVERT: B 129 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7604 (mmm160) REVERT: B 210 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9048 (tp) REVERT: B 217 MET cc_start: 0.8427 (ptm) cc_final: 0.8094 (ttt) REVERT: B 275 SER cc_start: 0.8752 (m) cc_final: 0.8514 (m) REVERT: B 292 PHE cc_start: 0.7933 (m-10) cc_final: 0.7340 (m-80) REVERT: B 325 MET cc_start: 0.8907 (tpp) cc_final: 0.8696 (tpp) REVERT: C 22 GLU cc_start: 0.7307 (tp30) cc_final: 0.7031 (tp30) REVERT: D 59 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6988 (mm110) REVERT: R 80 ARG cc_start: 0.7527 (tpp80) cc_final: 0.7222 (mmp80) REVERT: R 104 TRP cc_start: 0.7341 (t-100) cc_final: 0.6837 (t-100) REVERT: R 209 MET cc_start: 0.7682 (mmm) cc_final: 0.7278 (mmm) REVERT: R 216 GLN cc_start: 0.7972 (tp40) cc_final: 0.7297 (tm-30) REVERT: R 226 ILE cc_start: 0.9203 (tt) cc_final: 0.8861 (tt) REVERT: R 293 ASP cc_start: 0.9122 (t0) cc_final: 0.8853 (t0) REVERT: R 319 GLN cc_start: 0.7261 (tp40) cc_final: 0.6977 (tp-100) REVERT: S 3 GLN cc_start: 0.8087 (pt0) cc_final: 0.7856 (pt0) REVERT: S 47 TRP cc_start: 0.8302 (t60) cc_final: 0.8082 (t60) REVERT: S 86 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8849 (pp) REVERT: S 91 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7954 (t) REVERT: S 219 GLN cc_start: 0.9117 (pp30) cc_final: 0.8672 (pp30) outliers start: 49 outliers final: 41 residues processed: 266 average time/residue: 0.0943 time to fit residues: 34.6822 Evaluate side-chains 266 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 224 CYS 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 160 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 54 VAL 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 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 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 327 LYS 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 Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125303 restraints weight = 14528.965| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.89 r_work: 0.3505 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9777 Z= 0.130 Angle : 0.667 10.397 13260 Z= 0.331 Chirality : 0.043 0.253 1531 Planarity : 0.004 0.085 1660 Dihedral : 4.834 33.281 1336 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.57 % Allowed : 26.26 % Favored : 69.16 % 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: 0.17 (0.27), residues: 398 sheet: -1.63 (0.30), residues: 288 loop : -1.59 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.011 0.001 TYR S 178 PHE 0.017 0.001 PHE R 97 TRP 0.037 0.002 TRP S 111 HIS 0.020 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9771) covalent geometry : angle 0.66620 / 0.33 (13248) SS BOND : bond 0.00173 / 0.09 ( 6) SS BOND : angle 0.96072 / 0.53 ( 12) hydrogen bonds : bond 0.02915 / 1.89 ( 358) hydrogen bonds : angle 4.44826 / 3.07 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.77 seconds wall clock time: 43 minutes 17.09 seconds (2597.09 seconds total)