Starting phenix.real_space_refine on Tue Jul 29 08:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_0879.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_0879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_0879.map" model { file = "/net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_0879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lfo_0879/07_2025/6lfo_0879.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 6.69, per 1000 atoms: 0.70 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.30 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: 3.19 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2964 1.33 - 1.46: 2130 1.46 - 1.58: 4581 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9771 Sorted by residual: bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.89e+00 bond pdb=" CB VAL S 97 " pdb=" CG2 VAL S 97 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.28e+00 bond pdb=" CB TRP S 47 " pdb=" CG TRP S 47 " ideal model delta sigma weight residual 1.498 1.416 0.082 3.10e-02 1.04e+03 7.01e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.55e+00 bond pdb=" CG LEU B 168 " pdb=" CD1 LEU B 168 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 12910 3.00 - 6.01: 297 6.01 - 9.01: 30 9.01 - 12.01: 9 12.01 - 15.01: 2 Bond angle restraints: 13248 Sorted by residual: angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" CA LEU R 44 " pdb=" CB LEU R 44 " pdb=" CG LEU R 44 " ideal model delta sigma weight residual 116.30 131.31 -15.01 3.50e+00 8.16e-02 1.84e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5171 17.97 - 35.93: 591 35.93 - 53.90: 90 53.90 - 71.86: 15 71.86 - 89.83: 8 Dihedral angle restraints: 5875 sinusoidal: 2309 harmonic: 3566 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -134.87 -45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 34 " pdb=" CB CYS D 34 " ideal model delta sinusoidal sigma weight residual -86.00 -143.72 57.72 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1113 0.064 - 0.128: 356 0.128 - 0.192: 49 0.192 - 0.257: 11 0.257 - 0.321: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB THR A 181 " pdb=" CA THR A 181 " pdb=" OG1 THR A 181 " pdb=" CG2 THR A 181 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA MET A 240 " pdb=" N MET A 240 " pdb=" C MET A 240 " pdb=" CB MET A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1528 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 31 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 178 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C TYR S 178 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR S 178 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG S 179 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 112 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.44e+00 pdb=" CG TRP R 112 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 112 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP R 112 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 112 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 112 " 0.003 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2646 2.78 - 3.31: 8372 3.31 - 3.84: 15614 3.84 - 4.37: 17999 4.37 - 4.90: 31225 Nonbonded interactions: 75856 Sorted by model distance: nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.255 3.040 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 228 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.305 3.120 nonbonded pdb=" OG SER S 149 " pdb=" N SER S 150 " model vdw 2.308 3.120 ... (remaining 75851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.116 9777 Z= 0.570 Angle : 1.134 15.015 13260 Z= 0.595 Chirality : 0.062 0.321 1531 Planarity : 0.007 0.107 1660 Dihedral : 15.003 89.828 3553 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.035 0.004 TRP R 112 HIS 0.010 0.002 HIS B 91 PHE 0.023 0.003 PHE B 235 TYR 0.033 0.003 TYR S 178 ARG 0.011 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.29978 ( 358) hydrogen bonds : angle 10.83373 ( 1035) SS BOND : bond 0.01034 ( 6) SS BOND : angle 1.68996 ( 12) covalent geometry : bond 0.01281 ( 9771) covalent geometry : angle 1.13316 (13248) *********************** 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 : 1.162 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: 0.7534 (tt) REVERT: A 243 MET cc_start: 0.8964 (tpp) cc_final: 0.8726 (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: 0.2830 time to fit residues: 113.9044 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 : 1.138 ------------------------------------------------------------------------------- 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 101 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4027 r_free = 0.4027 target = 0.158190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120180 restraints weight = 14337.211| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.01 r_work: 0.3413 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9777 Z= 0.140 Angle : 0.656 8.729 13260 Z= 0.339 Chirality : 0.042 0.164 1531 Planarity : 0.005 0.091 1660 Dihedral : 5.922 38.628 1395 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.92 % Allowed : 18.68 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.20), residues: 1212 helix: -2.69 (0.20), residues: 398 sheet: -2.91 (0.27), residues: 292 loop : -2.71 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 112 HIS 0.002 0.001 HIS R 247 PHE 0.011 0.001 PHE A 334 TYR 0.025 0.001 TYR S 178 ARG 0.007 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 358) hydrogen bonds : angle 5.73192 ( 1035) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.59656 ( 12) covalent geometry : bond 0.00305 ( 9771) covalent geometry : angle 0.65467 (13248) *********************** 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 319 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.060 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: 0.7996 (mtt-85) cc_final: 0.7493 (mtm110) REVERT: A 232 LEU cc_start: 0.8848 (tt) cc_final: 0.8411 (tt) REVERT: A 296 TYR cc_start: 0.8575 (t80) cc_final: 0.8366 (t80) REVERT: A 304 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 310 LEU cc_start: 0.8963 (mt) cc_final: 0.8562 (mt) REVERT: B 9 GLN cc_start: 0.8262 (mm110) cc_final: 0.8011 (mp10) REVERT: B 15 LYS cc_start: 0.9111 (tptt) cc_final: 0.8785 (mtpp) REVERT: B 17 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 129 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7595 (mmm160) REVERT: B 159 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 292 PHE cc_start: 0.8069 (m-10) cc_final: 0.7638 (m-80) REVERT: B 297 TRP cc_start: 0.8869 (m100) cc_final: 0.8667 (m100) REVERT: B 335 PHE cc_start: 0.9068 (m-80) cc_final: 0.8832 (m-10) REVERT: C 38 MET cc_start: 0.8898 (ttp) cc_final: 0.8663 (ttp) REVERT: D 39 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6477 (tp) REVERT: R 63 LEU cc_start: 0.7848 (mm) cc_final: 0.7443 (mm) REVERT: R 173 SER cc_start: 0.9129 (t) cc_final: 0.8912 (p) REVERT: R 209 MET cc_start: 0.7608 (mmm) cc_final: 0.7077 (mmm) REVERT: R 226 ILE cc_start: 0.9179 (tt) cc_final: 0.8826 (tt) REVERT: R 242 HIS cc_start: 0.7787 (p90) cc_final: 0.7528 (p-80) REVERT: S 3 GLN cc_start: 0.8248 (pt0) cc_final: 0.7973 (pt0) REVERT: S 219 GLN cc_start: 0.9188 (pp30) cc_final: 0.8818 (pp30) REVERT: S 232 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7858 (ttpp) outliers start: 30 outliers final: 13 residues processed: 305 average time/residue: 0.2249 time to fit residues: 93.0738 Evaluate side-chains 256 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 144 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN R 306 HIS S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120781 restraints weight = 14623.839| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.91 r_work: 0.3433 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9777 Z= 0.111 Angle : 0.621 9.247 13260 Z= 0.313 Chirality : 0.042 0.144 1531 Planarity : 0.004 0.088 1660 Dihedral : 5.273 36.738 1392 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.99 % Allowed : 19.55 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.22), residues: 1212 helix: -1.69 (0.23), residues: 406 sheet: -2.43 (0.28), residues: 288 loop : -2.45 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 112 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE A 334 TYR 0.020 0.001 TYR S 178 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 358) hydrogen bonds : angle 4.90018 ( 1035) SS BOND : bond 0.00241 ( 6) SS BOND : angle 1.10231 ( 12) covalent geometry : bond 0.00244 ( 9771) covalent geometry : angle 0.62052 (13248) *********************** 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 312 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7491 (mtm110) REVERT: A 35 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8547 (mttm) REVERT: A 243 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8194 (mmm) REVERT: A 304 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 310 LEU cc_start: 0.9048 (mt) cc_final: 0.8613 (mt) REVERT: A 341 ASP cc_start: 0.8784 (t70) cc_final: 0.8374 (t0) REVERT: B 15 LYS cc_start: 0.9099 (tptt) cc_final: 0.8791 (mmmt) REVERT: B 17 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 129 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7574 (mmm160) REVERT: B 211 TRP cc_start: 0.9249 (m100) cc_final: 0.8972 (m100) REVERT: B 258 ASP cc_start: 0.7487 (t0) cc_final: 0.7161 (t0) REVERT: B 292 PHE cc_start: 0.7952 (m-10) cc_final: 0.7390 (m-80) REVERT: B 297 TRP cc_start: 0.8933 (m100) cc_final: 0.8682 (m100) REVERT: C 11 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 18 GLN cc_start: 0.8409 (tp40) cc_final: 0.8116 (tp40) REVERT: R 63 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7514 (mm) REVERT: R 95 LEU cc_start: 0.8492 (tp) cc_final: 0.8155 (pp) REVERT: R 126 LYS cc_start: 0.7469 (ttmm) cc_final: 0.7002 (tppt) REVERT: R 137 LEU cc_start: 0.8261 (mp) cc_final: 0.7944 (mp) REVERT: R 183 PHE cc_start: 0.8690 (m-80) cc_final: 0.8296 (m-80) REVERT: R 209 MET cc_start: 0.7638 (mmm) cc_final: 0.7166 (mmm) REVERT: R 216 GLN cc_start: 0.7854 (tp40) cc_final: 0.6935 (tm-30) REVERT: R 226 ILE cc_start: 0.9105 (tt) cc_final: 0.8770 (tt) REVERT: R 242 HIS cc_start: 0.7735 (p90) cc_final: 0.7406 (p-80) REVERT: S 3 GLN cc_start: 0.8107 (pt0) cc_final: 0.7836 (pt0) REVERT: S 91 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7900 (t) REVERT: S 219 GLN cc_start: 0.9214 (pp30) cc_final: 0.8765 (pp30) REVERT: S 232 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7732 (ttpp) outliers start: 41 outliers final: 23 residues processed: 295 average time/residue: 0.2727 time to fit residues: 110.2305 Evaluate side-chains 270 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 243 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115495 restraints weight = 14233.399| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.77 r_work: 0.3363 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9777 Z= 0.201 Angle : 0.673 8.965 13260 Z= 0.339 Chirality : 0.044 0.156 1531 Planarity : 0.004 0.087 1660 Dihedral : 5.278 34.161 1392 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.35 % Allowed : 21.30 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.23), residues: 1212 helix: -1.18 (0.24), residues: 412 sheet: -2.30 (0.28), residues: 290 loop : -2.21 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 112 HIS 0.004 0.001 HIS R 306 PHE 0.014 0.002 PHE B 335 TYR 0.029 0.002 TYR S 178 ARG 0.003 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 358) hydrogen bonds : angle 4.71698 ( 1035) SS BOND : bond 0.00233 ( 6) SS BOND : angle 1.13681 ( 12) covalent geometry : bond 0.00466 ( 9771) covalent geometry : angle 0.67257 (13248) *********************** 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 302 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7633 (mtm110) REVERT: A 216 GLU cc_start: 0.8394 (tt0) cc_final: 0.7988 (tt0) REVERT: A 243 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: A 277 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7696 (ttmt) REVERT: A 304 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 310 LEU cc_start: 0.9142 (mt) cc_final: 0.8667 (mt) REVERT: B 9 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7749 (mp10) REVERT: B 15 LYS cc_start: 0.9032 (tptt) cc_final: 0.8583 (ttmm) REVERT: B 17 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8188 (tm-30) REVERT: B 129 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7455 (mmm160) REVERT: B 172 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: B 258 ASP cc_start: 0.7419 (t0) cc_final: 0.6937 (t0) REVERT: B 275 SER cc_start: 0.8824 (m) cc_final: 0.8586 (m) REVERT: B 292 PHE cc_start: 0.8425 (m-10) cc_final: 0.7985 (m-80) REVERT: B 325 MET cc_start: 0.8915 (tpp) cc_final: 0.8602 (tpp) REVERT: C 11 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8853 (tm-30) REVERT: C 13 ARG cc_start: 0.8683 (ptm160) cc_final: 0.8438 (ptp-170) REVERT: R 63 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7495 (mm) REVERT: R 95 LEU cc_start: 0.8521 (tp) cc_final: 0.8021 (pp) REVERT: R 126 LYS cc_start: 0.7529 (ttmm) cc_final: 0.6887 (ttpt) REVERT: R 137 LEU cc_start: 0.8503 (mp) cc_final: 0.8268 (mp) REVERT: R 209 MET cc_start: 0.7706 (mmm) cc_final: 0.7218 (mmm) REVERT: R 216 GLN cc_start: 0.7882 (tp40) cc_final: 0.7084 (tm-30) REVERT: R 226 ILE cc_start: 0.9155 (tt) cc_final: 0.8819 (tt) REVERT: S 3 GLN cc_start: 0.8204 (pt0) cc_final: 0.7976 (pt0) REVERT: S 20 LEU cc_start: 0.8003 (mm) cc_final: 0.7499 (mm) REVERT: S 91 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7985 (t) REVERT: S 219 GLN cc_start: 0.9223 (pp30) cc_final: 0.8807 (pp30) REVERT: S 235 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6024 (mm) outliers start: 55 outliers final: 37 residues processed: 285 average time/residue: 0.2232 time to fit residues: 87.2544 Evaluate side-chains 267 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 185 VAL 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 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU 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 312 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121191 restraints weight = 14340.381| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.06 r_work: 0.3390 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3694 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= 0.125 Angle : 0.620 8.744 13260 Z= 0.310 Chirality : 0.042 0.150 1531 Planarity : 0.004 0.087 1660 Dihedral : 5.071 35.181 1392 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.77 % Allowed : 22.57 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1212 helix: -0.71 (0.25), residues: 399 sheet: -2.10 (0.29), residues: 298 loop : -2.05 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 264 HIS 0.005 0.001 HIS R 306 PHE 0.015 0.001 PHE R 97 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 358) hydrogen bonds : angle 4.46750 ( 1035) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.98424 ( 12) covalent geometry : bond 0.00285 ( 9771) covalent geometry : angle 0.61956 (13248) *********************** 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 299 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7616 (mtm110) REVERT: A 216 GLU cc_start: 0.8395 (tt0) cc_final: 0.8007 (tt0) REVERT: A 277 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7752 (ttmt) REVERT: A 304 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 310 LEU cc_start: 0.9125 (mt) cc_final: 0.8602 (mt) REVERT: B 9 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7979 (mp10) REVERT: B 15 LYS cc_start: 0.9020 (tptt) cc_final: 0.8555 (ttmm) REVERT: B 17 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 61 MET cc_start: 0.8840 (ppp) cc_final: 0.8230 (ppp) REVERT: B 124 TYR cc_start: 0.9012 (m-80) cc_final: 0.8764 (m-10) REVERT: B 129 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.7567 (mmm160) REVERT: B 210 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9113 (tp) REVERT: B 215 GLU cc_start: 0.8681 (mp0) cc_final: 0.8454 (mp0) REVERT: B 275 SER cc_start: 0.8784 (m) cc_final: 0.8530 (m) REVERT: B 292 PHE cc_start: 0.8209 (m-10) cc_final: 0.7645 (m-80) REVERT: B 325 MET cc_start: 0.8851 (tpp) cc_final: 0.8564 (tpp) REVERT: C 11 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8803 (tm-30) REVERT: C 22 GLU cc_start: 0.7494 (tp30) cc_final: 0.7258 (tp30) REVERT: R 63 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7446 (mm) REVERT: R 95 LEU cc_start: 0.8569 (tp) cc_final: 0.8092 (pp) REVERT: R 126 LYS cc_start: 0.7405 (ttmm) cc_final: 0.6880 (ttpt) REVERT: R 209 MET cc_start: 0.7691 (mmm) cc_final: 0.7336 (mmm) REVERT: R 216 GLN cc_start: 0.7757 (tp40) cc_final: 0.7159 (tm-30) REVERT: R 226 ILE cc_start: 0.9097 (tt) cc_final: 0.8704 (tt) REVERT: R 293 ASP cc_start: 0.9152 (t0) cc_final: 0.8876 (t0) REVERT: S 3 GLN cc_start: 0.8156 (pt0) cc_final: 0.7911 (pt0) REVERT: S 86 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8818 (pp) REVERT: S 91 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8020 (t) REVERT: S 219 GLN cc_start: 0.9171 (pp30) cc_final: 0.8799 (pp30) REVERT: S 235 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5828 (mm) outliers start: 49 outliers final: 28 residues processed: 279 average time/residue: 0.2332 time to fit residues: 88.7566 Evaluate side-chains 264 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 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 162 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119968 restraints weight = 14396.836| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.92 r_work: 0.3402 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3911 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= 0.114 Angle : 0.622 10.580 13260 Z= 0.308 Chirality : 0.042 0.146 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.894 33.987 1392 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.47 % Allowed : 22.86 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.23), residues: 1212 helix: -0.44 (0.26), residues: 399 sheet: -1.90 (0.29), residues: 289 loop : -1.97 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 112 HIS 0.005 0.001 HIS R 306 PHE 0.013 0.001 PHE R 97 TYR 0.024 0.001 TYR S 178 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 358) hydrogen bonds : angle 4.37423 ( 1035) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.95990 ( 12) covalent geometry : bond 0.00255 ( 9771) covalent geometry : angle 0.62133 (13248) *********************** 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 296 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7381 (mtm110) REVERT: A 216 GLU cc_start: 0.8395 (tt0) cc_final: 0.8004 (tt0) REVERT: A 277 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7808 (ttmt) REVERT: A 304 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 308 GLU cc_start: 0.8271 (tt0) cc_final: 0.8059 (tt0) REVERT: B 8 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7494 (mtm-85) REVERT: B 15 LYS cc_start: 0.9002 (tptt) cc_final: 0.8547 (ttmm) REVERT: B 17 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 61 MET cc_start: 0.8854 (ppp) cc_final: 0.8194 (ppp) REVERT: B 124 TYR cc_start: 0.8997 (m-80) cc_final: 0.8751 (m-10) REVERT: B 129 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7552 (mmm160) REVERT: B 172 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: B 210 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 275 SER cc_start: 0.8817 (m) cc_final: 0.8598 (m) REVERT: B 292 PHE cc_start: 0.8099 (m-10) cc_final: 0.7529 (m-80) REVERT: B 322 ASP cc_start: 0.8456 (t0) cc_final: 0.8250 (t0) REVERT: B 325 MET cc_start: 0.8858 (tpp) cc_final: 0.8555 (tpp) REVERT: C 11 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8792 (tm-30) REVERT: C 13 ARG cc_start: 0.8759 (ptm160) cc_final: 0.7303 (ptp-110) REVERT: C 22 GLU cc_start: 0.7594 (tp30) cc_final: 0.7343 (tp30) REVERT: C 27 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7585 (mtt-85) REVERT: R 63 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7462 (mm) REVERT: R 126 LYS cc_start: 0.7328 (ttmm) cc_final: 0.6838 (ttpt) REVERT: R 137 LEU cc_start: 0.8382 (mp) cc_final: 0.8110 (mp) REVERT: R 209 MET cc_start: 0.7676 (mmm) cc_final: 0.7330 (mmm) REVERT: R 216 GLN cc_start: 0.7761 (tp40) cc_final: 0.7183 (pp30) REVERT: R 226 ILE cc_start: 0.9146 (tt) cc_final: 0.8794 (tt) REVERT: R 293 ASP cc_start: 0.9150 (t0) cc_final: 0.8874 (t0) REVERT: S 3 GLN cc_start: 0.8184 (pt0) cc_final: 0.7969 (pt0) REVERT: S 86 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8800 (pp) REVERT: S 91 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8045 (t) REVERT: S 219 GLN cc_start: 0.9164 (pp30) cc_final: 0.8753 (pp30) REVERT: S 235 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5683 (mm) outliers start: 46 outliers final: 31 residues processed: 282 average time/residue: 0.2750 time to fit residues: 106.8789 Evaluate side-chains 270 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 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 Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4045 r_free = 0.4045 target = 0.159532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121850 restraints weight = 14491.954| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.92 r_work: 0.3438 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9777 Z= 0.120 Angle : 0.637 12.238 13260 Z= 0.312 Chirality : 0.043 0.278 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.840 33.878 1392 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.38 % Allowed : 23.83 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1212 helix: -0.26 (0.26), residues: 403 sheet: -1.85 (0.30), residues: 288 loop : -1.86 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 112 HIS 0.005 0.001 HIS R 306 PHE 0.017 0.001 PHE S 68 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 358) hydrogen bonds : angle 4.31613 ( 1035) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.96327 ( 12) covalent geometry : bond 0.00275 ( 9771) covalent geometry : angle 0.63646 (13248) *********************** 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 279 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7425 (mtm110) REVERT: A 216 GLU cc_start: 0.8378 (tt0) cc_final: 0.8109 (tt0) REVERT: A 277 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7764 (ttmt) REVERT: A 304 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 15 LYS cc_start: 0.9040 (tptt) cc_final: 0.8590 (ttmm) REVERT: B 17 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 61 MET cc_start: 0.8771 (ppp) cc_final: 0.8127 (ppp) REVERT: B 129 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7570 (mmm160) REVERT: B 134 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8381 (ptt-90) REVERT: B 210 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 258 ASP cc_start: 0.7485 (t0) cc_final: 0.7184 (t0) REVERT: B 275 SER cc_start: 0.8842 (m) cc_final: 0.8614 (m) REVERT: B 292 PHE cc_start: 0.8127 (m-10) cc_final: 0.7539 (m-80) REVERT: B 325 MET cc_start: 0.8863 (tpp) cc_final: 0.8568 (tpp) REVERT: C 11 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8773 (tm-30) REVERT: C 22 GLU cc_start: 0.7575 (tp30) cc_final: 0.7285 (tp30) REVERT: C 27 ARG cc_start: 0.7800 (mtt90) cc_final: 0.6963 (mmt90) REVERT: R 63 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7449 (mm) REVERT: R 126 LYS cc_start: 0.7309 (ttmm) cc_final: 0.6850 (ttpt) REVERT: R 209 MET cc_start: 0.7663 (mmm) cc_final: 0.7307 (mmm) REVERT: R 216 GLN cc_start: 0.7974 (tp40) cc_final: 0.7221 (tm-30) REVERT: R 226 ILE cc_start: 0.9126 (tt) cc_final: 0.8774 (tt) REVERT: R 293 ASP cc_start: 0.9143 (t0) cc_final: 0.8858 (t0) REVERT: S 3 GLN cc_start: 0.8159 (pt0) cc_final: 0.7934 (pt0) REVERT: S 86 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8761 (pp) REVERT: S 91 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (t) REVERT: S 219 GLN cc_start: 0.9141 (pp30) cc_final: 0.8712 (pp30) REVERT: S 235 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5717 (mm) outliers start: 45 outliers final: 36 residues processed: 265 average time/residue: 0.3199 time to fit residues: 119.0156 Evaluate side-chains 257 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 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 R residue 312 LEU 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 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4056 r_free = 0.4056 target = 0.160449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121134 restraints weight = 14534.655| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.93 r_work: 0.3439 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9777 Z= 0.112 Angle : 0.635 12.755 13260 Z= 0.311 Chirality : 0.042 0.264 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.745 33.386 1392 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.67 % Allowed : 23.54 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1212 helix: -0.06 (0.26), residues: 401 sheet: -1.73 (0.30), residues: 287 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 111 HIS 0.008 0.001 HIS A 188 PHE 0.011 0.001 PHE R 97 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 358) hydrogen bonds : angle 4.31389 ( 1035) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.86665 ( 12) covalent geometry : bond 0.00255 ( 9771) covalent geometry : angle 0.63508 (13248) *********************** 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 282 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7809 (mtt-85) cc_final: 0.7413 (mtm110) REVERT: A 216 GLU cc_start: 0.8326 (tt0) cc_final: 0.8091 (tt0) REVERT: A 304 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 15 LYS cc_start: 0.9038 (tptt) cc_final: 0.8560 (ttmm) REVERT: B 61 MET cc_start: 0.8811 (ppp) cc_final: 0.8195 (ppp) REVERT: B 129 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7513 (mmm160) REVERT: B 134 ARG cc_start: 0.8791 (ptt-90) cc_final: 0.8422 (ptt-90) REVERT: B 209 LYS cc_start: 0.9030 (mttm) cc_final: 0.8618 (mttt) REVERT: B 210 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9094 (tp) REVERT: B 211 TRP cc_start: 0.9158 (m100) cc_final: 0.8915 (m100) REVERT: B 215 GLU cc_start: 0.8773 (mp0) cc_final: 0.8117 (pm20) REVERT: B 258 ASP cc_start: 0.7305 (t0) cc_final: 0.7077 (t0) REVERT: B 275 SER cc_start: 0.8844 (m) cc_final: 0.8618 (m) REVERT: B 292 PHE cc_start: 0.8067 (m-10) cc_final: 0.7448 (m-80) REVERT: B 325 MET cc_start: 0.8914 (tpp) cc_final: 0.8624 (tpp) REVERT: C 22 GLU cc_start: 0.7556 (tp30) cc_final: 0.7225 (tp30) REVERT: C 27 ARG cc_start: 0.7765 (mtt90) cc_final: 0.6988 (mmt90) REVERT: D 38 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: R 63 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7401 (mm) REVERT: R 104 TRP cc_start: 0.7204 (t-100) cc_final: 0.6806 (t-100) REVERT: R 126 LYS cc_start: 0.7049 (ttmm) cc_final: 0.6527 (ttpt) REVERT: R 209 MET cc_start: 0.7746 (mmm) cc_final: 0.7213 (mmm) REVERT: R 216 GLN cc_start: 0.7949 (tp40) cc_final: 0.7260 (tm-30) REVERT: R 226 ILE cc_start: 0.9176 (tt) cc_final: 0.8844 (tt) REVERT: R 293 ASP cc_start: 0.9145 (t0) cc_final: 0.8862 (t0) REVERT: S 3 GLN cc_start: 0.8100 (pt0) cc_final: 0.7866 (pt0) REVERT: S 86 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8694 (pp) REVERT: S 91 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8032 (t) REVERT: S 219 GLN cc_start: 0.9124 (pp30) cc_final: 0.8715 (pp30) REVERT: S 235 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5698 (mm) outliers start: 48 outliers final: 36 residues processed: 263 average time/residue: 0.3205 time to fit residues: 121.6975 Evaluate side-chains 261 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU 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 312 LEU 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 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 0.0370 chunk 92 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS S 39 GLN ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116755 restraints weight = 14439.305| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.62 r_work: 0.3399 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9777 Z= 0.174 Angle : 0.676 11.442 13260 Z= 0.333 Chirality : 0.044 0.252 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.979 33.360 1392 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.47 % Allowed : 23.93 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.24), residues: 1212 helix: 0.00 (0.26), residues: 401 sheet: -1.79 (0.30), residues: 293 loop : -1.69 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 111 HIS 0.019 0.001 HIS A 188 PHE 0.018 0.001 PHE S 68 TYR 0.014 0.002 TYR S 178 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 358) hydrogen bonds : angle 4.39309 ( 1035) SS BOND : bond 0.00161 ( 6) SS BOND : angle 1.13791 ( 12) covalent geometry : bond 0.00404 ( 9771) covalent geometry : angle 0.67510 (13248) *********************** 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 273 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7498 (mtm110) REVERT: A 277 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7570 (ttmt) REVERT: A 304 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 15 LYS cc_start: 0.9044 (tptt) cc_final: 0.8515 (ttmm) REVERT: B 61 MET cc_start: 0.8740 (ppp) cc_final: 0.8141 (ppp) REVERT: B 129 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7563 (mmm160) REVERT: B 134 ARG cc_start: 0.8670 (ptt-90) cc_final: 0.8262 (ptt-90) REVERT: B 171 ILE cc_start: 0.8255 (mm) cc_final: 0.8029 (mm) REVERT: B 172 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: B 209 LYS cc_start: 0.9066 (mttm) cc_final: 0.8774 (mttt) REVERT: B 210 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9146 (tp) REVERT: B 275 SER cc_start: 0.8969 (m) cc_final: 0.8755 (m) REVERT: B 292 PHE cc_start: 0.8359 (m-10) cc_final: 0.7821 (m-80) REVERT: B 325 MET cc_start: 0.8865 (tpp) cc_final: 0.8603 (tpp) REVERT: C 22 GLU cc_start: 0.7578 (tp30) cc_final: 0.7248 (tp30) REVERT: C 27 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7243 (mtt90) REVERT: R 63 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7388 (mm) REVERT: R 90 LEU cc_start: 0.8020 (tp) cc_final: 0.7582 (tt) REVERT: R 104 TRP cc_start: 0.7405 (t-100) cc_final: 0.6947 (t-100) REVERT: R 126 LYS cc_start: 0.7218 (ttmm) cc_final: 0.6565 (ttpt) REVERT: R 137 LEU cc_start: 0.8399 (mp) cc_final: 0.8111 (mp) REVERT: R 209 MET cc_start: 0.7804 (mmm) cc_final: 0.7270 (mmm) REVERT: R 216 GLN cc_start: 0.7923 (tp40) cc_final: 0.7211 (tm-30) REVERT: R 226 ILE cc_start: 0.9128 (tt) cc_final: 0.8778 (tt) REVERT: R 293 ASP cc_start: 0.9129 (t0) cc_final: 0.8842 (t0) REVERT: S 3 GLN cc_start: 0.7974 (pt0) cc_final: 0.7747 (pt0) REVERT: S 20 LEU cc_start: 0.7625 (mm) cc_final: 0.7225 (mm) REVERT: S 86 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8690 (pp) REVERT: S 91 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8016 (t) REVERT: S 219 GLN cc_start: 0.9147 (pp30) cc_final: 0.8690 (pp30) outliers start: 46 outliers final: 38 residues processed: 257 average time/residue: 0.2290 time to fit residues: 80.4179 Evaluate side-chains 256 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 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 312 LEU 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 97 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4043 r_free = 0.4043 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119943 restraints weight = 14373.285| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.86 r_work: 0.3423 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9777 Z= 0.130 Angle : 0.672 12.765 13260 Z= 0.330 Chirality : 0.043 0.254 1531 Planarity : 0.004 0.085 1660 Dihedral : 4.904 35.074 1392 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.28 % Allowed : 24.12 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1212 helix: 0.05 (0.26), residues: 403 sheet: -1.74 (0.30), residues: 292 loop : -1.69 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 111 HIS 0.013 0.001 HIS A 188 PHE 0.013 0.001 PHE R 97 TYR 0.015 0.001 TYR S 215 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 358) hydrogen bonds : angle 4.32953 ( 1035) SS BOND : bond 0.00169 ( 6) SS BOND : angle 1.07523 ( 12) covalent geometry : bond 0.00300 ( 9771) covalent geometry : angle 0.67130 (13248) ********************** 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 271 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7394 (mtm110) REVERT: A 277 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7770 (ptmt) REVERT: A 304 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 15 LYS cc_start: 0.9045 (tptt) cc_final: 0.8567 (ttmm) REVERT: B 61 MET cc_start: 0.8844 (ppp) cc_final: 0.8267 (ppp) REVERT: B 129 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7546 (mmm160) REVERT: B 134 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8380 (ptt-90) REVERT: B 171 ILE cc_start: 0.8117 (mm) cc_final: 0.7852 (mm) REVERT: B 210 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9124 (tp) REVERT: B 211 TRP cc_start: 0.9176 (m100) cc_final: 0.8855 (m100) REVERT: B 275 SER cc_start: 0.8870 (m) cc_final: 0.8630 (m) REVERT: B 289 TYR cc_start: 0.8779 (m-80) cc_final: 0.8391 (m-80) REVERT: B 292 PHE cc_start: 0.8173 (m-10) cc_final: 0.7577 (m-80) REVERT: B 325 MET cc_start: 0.8871 (tpp) cc_final: 0.8597 (tpp) REVERT: C 11 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8743 (tm-30) REVERT: C 22 GLU cc_start: 0.7451 (tp30) cc_final: 0.7072 (tp30) REVERT: R 63 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7370 (mm) REVERT: R 104 TRP cc_start: 0.7319 (t-100) cc_final: 0.6849 (t-100) REVERT: R 126 LYS cc_start: 0.7193 (ttmm) cc_final: 0.6496 (ttpt) REVERT: R 209 MET cc_start: 0.7808 (mmm) cc_final: 0.7250 (mmm) REVERT: R 216 GLN cc_start: 0.7954 (tp40) cc_final: 0.7281 (tm-30) REVERT: R 226 ILE cc_start: 0.9126 (tt) cc_final: 0.8775 (tt) REVERT: R 293 ASP cc_start: 0.9122 (t0) cc_final: 0.8839 (t0) REVERT: S 3 GLN cc_start: 0.8139 (pt0) cc_final: 0.7919 (pt0) REVERT: S 20 LEU cc_start: 0.7582 (mm) cc_final: 0.7153 (mm) REVERT: S 86 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8711 (pp) REVERT: S 91 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8064 (t) REVERT: S 219 GLN cc_start: 0.9138 (pp30) cc_final: 0.8764 (pp30) outliers start: 44 outliers final: 35 residues processed: 256 average time/residue: 0.2264 time to fit residues: 79.5646 Evaluate side-chains 253 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 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 312 LEU 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 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 83 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 87 optimal weight: 0.0050 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 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 = 0.4064 r_free = 0.4064 target = 0.161349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121567 restraints weight = 14296.768| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.89 r_work: 0.3454 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9777 Z= 0.117 Angle : 0.659 12.529 13260 Z= 0.324 Chirality : 0.043 0.252 1531 Planarity : 0.004 0.086 1660 Dihedral : 4.795 34.969 1392 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.89 % Allowed : 25.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1212 helix: 0.16 (0.27), residues: 403 sheet: -1.66 (0.30), residues: 290 loop : -1.66 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 111 HIS 0.013 0.001 HIS A 188 PHE 0.011 0.001 PHE R 97 TYR 0.014 0.001 TYR A 296 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02831 ( 358) hydrogen bonds : angle 4.29084 ( 1035) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.98633 ( 12) covalent geometry : bond 0.00268 ( 9771) covalent geometry : angle 0.65895 (13248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5675.10 seconds wall clock time: 102 minutes 56.44 seconds (6176.44 seconds total)