Starting phenix.real_space_refine on Fri Mar 14 03:26:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323.map" model { file = "/net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jip_36323/03_2025/8jip_36323_neut_trim.cif" } resolution = 2.85 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5961 2.51 5 N 1609 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9362 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3109 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2016 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.46, per 1000 atoms: 0.58 Number of scatterers: 9362 At special positions: 0 Unit cell: (85.14, 100.62, 175.44, 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 57 16.00 O 1735 8.00 N 1609 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 41.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 31 through 51 Processing helix chain 'R' and resid 89 through 94 removed outlier: 3.745A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.505A pdb=" N THR R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 removed outlier: 3.561A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 199 " --> pdb=" O PHE R 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 222 removed outlier: 3.781A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU R 218 " --> pdb=" O TRP R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 232 removed outlier: 3.624A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 257 removed outlier: 3.973A pdb=" N CYS R 236 " --> pdb=" O LEU R 232 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 254 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE R 257 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.735A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.821A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.822A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 326 removed outlier: 3.890A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 344 through 349 Processing helix chain 'R' and resid 355 through 361 removed outlier: 4.331A pdb=" N LEU R 359 " --> pdb=" O THR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 377 through 402 removed outlier: 3.505A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.650A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 31 removed outlier: 3.519A pdb=" N GLN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.511A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.587A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.492A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.694A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.762A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.568A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.666A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'P' and resid 3 through 27 removed outlier: 3.515A pdb=" N GLN P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.763A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 42 removed outlier: 4.056A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.698A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.787A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.854A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.291A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.805A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.043A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.551A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.873A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.106A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.955A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 4.182A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.841A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 71 through 73 368 hydrogen bonds defined for protein. 1044 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: 3.36 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1531 1.30 - 1.43: 2611 1.43 - 1.55: 5351 1.55 - 1.68: 2 1.68 - 1.81: 77 Bond restraints: 9572 Sorted by residual: bond pdb=" C LEU R 218 " pdb=" O LEU R 218 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.22e-02 6.72e+03 3.08e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" C SER P 11 " pdb=" O SER P 11 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" CA SER P 11 " pdb=" C SER P 11 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.329 1.373 -0.044 1.18e-02 7.18e+03 1.37e+01 ... (remaining 9567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 12565 2.55 - 5.10: 341 5.10 - 7.65: 51 7.65 - 10.20: 17 10.20 - 12.75: 9 Bond angle restraints: 12983 Sorted by residual: angle pdb=" N ARG R 64 " pdb=" CA ARG R 64 " pdb=" C ARG R 64 " ideal model delta sigma weight residual 114.31 102.32 11.99 1.29e+00 6.01e-01 8.63e+01 angle pdb=" C THR A 292 " pdb=" N PRO A 293 " pdb=" CA PRO A 293 " ideal model delta sigma weight residual 120.66 111.89 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N THR R 353 " pdb=" CA THR R 353 " pdb=" C THR R 353 " ideal model delta sigma weight residual 114.04 104.13 9.91 1.24e+00 6.50e-01 6.39e+01 angle pdb=" N LEU R 379 " pdb=" CA LEU R 379 " pdb=" C LEU R 379 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.33e+01 angle pdb=" N PRO R 73 " pdb=" CA PRO R 73 " pdb=" C PRO R 73 " ideal model delta sigma weight residual 110.80 121.96 -11.16 1.51e+00 4.39e-01 5.46e+01 ... (remaining 12978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4808 17.82 - 35.64: 572 35.64 - 53.46: 204 53.46 - 71.28: 70 71.28 - 89.11: 17 Dihedral angle restraints: 5671 sinusoidal: 2226 harmonic: 3445 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -149.84 63.84 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1288 0.101 - 0.201: 134 0.201 - 0.302: 15 0.302 - 0.403: 4 0.403 - 0.504: 1 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ASN R 407 " pdb=" N ASN R 407 " pdb=" C ASN R 407 " pdb=" CB ASN R 407 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA ASN R 63 " pdb=" N ASN R 63 " pdb=" C ASN R 63 " pdb=" CB ASN R 63 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1439 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.039 2.00e-02 2.50e+03 4.74e-02 2.81e+01 pdb=" C04 D6M P 101 " 0.056 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.049 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.064 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 323 " 0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C ILE R 323 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE R 323 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE R 324 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 289 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C TYR R 289 " -0.071 2.00e-02 2.50e+03 pdb=" O TYR R 289 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU R 290 " 0.024 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 590 2.71 - 3.25: 9021 3.25 - 3.80: 14807 3.80 - 4.35: 18017 4.35 - 4.90: 30178 Nonbonded interactions: 72613 Sorted by model distance: nonbonded pdb=" N GLU A 276 " pdb=" OE1 GLU A 276 " model vdw 2.156 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.229 3.040 nonbonded pdb=" O LYS N 65 " pdb=" NH1 ARG N 67 " model vdw 2.252 3.120 nonbonded pdb=" O PHE R 385 " pdb=" OG SER R 389 " model vdw 2.255 3.040 ... (remaining 72608 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: 7.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.690 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.006 0.068 9572 Z= 0.403 Angle : 1.049 12.753 12983 Z= 0.699 Chirality : 0.066 0.504 1442 Planarity : 0.005 0.056 1654 Dihedral : 18.747 89.106 3425 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.62 % Favored : 92.61 % Rotamer: Outliers : 14.94 % Allowed : 9.23 % Favored : 75.83 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.27 (0.24), residues: 1164 helix: -1.39 (0.25), residues: 422 sheet: -0.30 (0.38), residues: 190 loop : -1.99 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.005 0.001 HIS R 99 PHE 0.016 0.002 PHE R 187 TYR 0.016 0.002 TYR A 56 ARG 0.004 0.000 ARG R 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 170 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 107 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.4396 (pm20) REVERT: R 112 GLN cc_start: 0.1989 (OUTLIER) cc_final: 0.1314 (mt0) REVERT: A 229 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 231 ASN cc_start: 0.9505 (t0) cc_final: 0.9303 (t0) REVERT: A 232 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8692 (mtp85) REVERT: A 359 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: P 1 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.7858 (p-80) REVERT: P 11 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8205 (t) REVERT: P 13 TYR cc_start: 0.9042 (t80) cc_final: 0.8752 (t80) REVERT: P 21 ASP cc_start: 0.9180 (m-30) cc_final: 0.8972 (m-30) REVERT: B 44 GLN cc_start: 0.7341 (mp-120) cc_final: 0.6841 (mp-120) REVERT: B 172 GLU cc_start: 0.9190 (tp30) cc_final: 0.8825 (tp30) REVERT: B 175 GLN cc_start: 0.8456 (mp10) cc_final: 0.8089 (mp10) REVERT: B 217 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6565 (pmt) REVERT: B 220 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: B 259 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8002 (tp40) REVERT: B 264 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: B 303 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (OUTLIER) REVERT: G 21 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7315 (pp-130) REVERT: N 43 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8575 (pmtt) outliers start: 149 outliers final: 42 residues processed: 284 average time/residue: 1.1676 time to fit residues: 354.4303 Evaluate side-chains 165 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 47 GLN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 421 ARG Chi-restraints excluded: chain R residue 423 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN R 82 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN R 221 GLN R 234 GLN R 338 ASN R 394 GLN R 406 ASN A 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084193 restraints weight = 17431.838| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.91 r_work: 0.2989 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9572 Z= 0.293 Angle : 0.700 8.888 12983 Z= 0.364 Chirality : 0.044 0.143 1442 Planarity : 0.005 0.048 1654 Dihedral : 10.619 75.690 1432 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 5.82 % Allowed : 19.46 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.26 (0.24), residues: 1164 helix: 0.05 (0.25), residues: 447 sheet: 0.18 (0.41), residues: 175 loop : -1.98 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 39 HIS 0.004 0.001 HIS A 324 PHE 0.034 0.002 PHE R 80 TYR 0.025 0.002 TYR R 289 ARG 0.008 0.001 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 263 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6553 (tm130) REVERT: R 348 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8182 (tpm-80) REVERT: R 414 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7693 (ttm110) REVERT: A 20 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8231 (tm-30) REVERT: A 171 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5343 (mp10) REVERT: A 231 ASN cc_start: 0.9545 (t0) cc_final: 0.9312 (t0) REVERT: B 172 GLU cc_start: 0.9408 (tp30) cc_final: 0.9080 (tp30) REVERT: B 175 GLN cc_start: 0.8722 (mp10) cc_final: 0.8242 (mp10) REVERT: B 260 GLU cc_start: 0.7988 (pp20) cc_final: 0.7768 (pp20) REVERT: B 301 LYS cc_start: 0.7588 (mppt) cc_final: 0.7153 (mmtm) REVERT: B 303 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: G 21 MET cc_start: 0.7147 (ppp) cc_final: 0.6898 (pp-130) REVERT: N 43 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8406 (pmtt) outliers start: 58 outliers final: 29 residues processed: 166 average time/residue: 1.1834 time to fit residues: 210.2102 Evaluate side-chains 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 414 ARG Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 0.0040 chunk 7 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN R 99 HIS R 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077742 restraints weight = 17568.228| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.92 r_work: 0.2877 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9572 Z= 0.458 Angle : 0.730 8.725 12983 Z= 0.388 Chirality : 0.047 0.206 1442 Planarity : 0.005 0.041 1654 Dihedral : 8.038 57.068 1353 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 5.72 % Allowed : 21.77 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.07 (0.24), residues: 1164 helix: 0.52 (0.25), residues: 450 sheet: -0.22 (0.38), residues: 195 loop : -2.06 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 39 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE N 108 TYR 0.024 0.002 TYR N 80 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: R 102 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6069 (mpp-170) REVERT: R 263 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6936 (tm-30) REVERT: R 348 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8216 (tpm-80) REVERT: R 414 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7728 (ttm110) REVERT: R 415 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7802 (mtmm) REVERT: A 231 ASN cc_start: 0.9532 (t0) cc_final: 0.9281 (t0) REVERT: B 172 GLU cc_start: 0.9439 (tp30) cc_final: 0.9169 (tp30) REVERT: B 175 GLN cc_start: 0.8662 (mp10) cc_final: 0.8179 (mp10) REVERT: B 217 MET cc_start: 0.8052 (pmm) cc_final: 0.7808 (pmm) REVERT: B 260 GLU cc_start: 0.8340 (pp20) cc_final: 0.7918 (pp20) REVERT: G 21 MET cc_start: 0.7307 (ppp) cc_final: 0.7065 (pp-130) REVERT: G 42 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7220 (mt-10) outliers start: 57 outliers final: 30 residues processed: 154 average time/residue: 1.5574 time to fit residues: 256.2734 Evaluate side-chains 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 414 ARG Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081064 restraints weight = 17462.797| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.99 r_work: 0.2938 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9572 Z= 0.220 Angle : 0.603 10.263 12983 Z= 0.313 Chirality : 0.042 0.176 1442 Planarity : 0.004 0.040 1654 Dihedral : 7.167 59.920 1339 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 3.91 % Allowed : 25.28 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.60 (0.25), residues: 1164 helix: 1.08 (0.26), residues: 447 sheet: 0.21 (0.41), residues: 180 loop : -1.97 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.003 0.000 HIS R 171 PHE 0.018 0.001 PHE R 156 TYR 0.018 0.001 TYR R 148 ARG 0.015 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 102 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6167 (mpp-170) REVERT: R 224 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8781 (tm) REVERT: R 348 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8155 (tpm-80) REVERT: R 414 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7664 (ttm110) REVERT: A 18 MET cc_start: 0.9102 (tpp) cc_final: 0.8896 (ttm) REVERT: A 231 ASN cc_start: 0.9499 (t0) cc_final: 0.9138 (m110) REVERT: B 172 GLU cc_start: 0.9423 (tp30) cc_final: 0.9134 (tp30) REVERT: B 175 GLN cc_start: 0.8685 (mp10) cc_final: 0.8157 (mp10) REVERT: B 217 MET cc_start: 0.8011 (pmm) cc_final: 0.7774 (pmm) REVERT: G 21 MET cc_start: 0.7236 (ppp) cc_final: 0.7013 (pp-130) REVERT: G 42 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7107 (mt-10) outliers start: 39 outliers final: 19 residues processed: 147 average time/residue: 1.1579 time to fit residues: 182.5509 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 414 ARG Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.130945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081087 restraints weight = 17352.081| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.92 r_work: 0.2938 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9572 Z= 0.223 Angle : 0.604 9.517 12983 Z= 0.313 Chirality : 0.042 0.214 1442 Planarity : 0.003 0.037 1654 Dihedral : 6.768 59.921 1337 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 4.31 % Allowed : 25.68 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.36 (0.25), residues: 1164 helix: 1.36 (0.26), residues: 448 sheet: 0.26 (0.41), residues: 182 loop : -1.91 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.016 0.001 PHE R 156 TYR 0.018 0.001 TYR R 148 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 224 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8650 (tm) REVERT: R 263 GLN cc_start: 0.7710 (pm20) cc_final: 0.7167 (tm-30) REVERT: R 348 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (tpm-80) REVERT: R 414 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7689 (ttm110) REVERT: A 18 MET cc_start: 0.9152 (tpp) cc_final: 0.8889 (ttm) REVERT: A 20 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8291 (tm-30) REVERT: A 231 ASN cc_start: 0.9485 (t0) cc_final: 0.9148 (m110) REVERT: A 284 ARG cc_start: 0.8694 (mpp80) cc_final: 0.8427 (mpt-90) REVERT: B 9 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: B 172 GLU cc_start: 0.9419 (tp30) cc_final: 0.9141 (tp30) REVERT: B 175 GLN cc_start: 0.8702 (mp10) cc_final: 0.8177 (mp10) REVERT: B 217 MET cc_start: 0.8051 (pmm) cc_final: 0.7798 (pmm) REVERT: B 260 GLU cc_start: 0.8291 (pp20) cc_final: 0.8010 (pp20) REVERT: G 21 MET cc_start: 0.7248 (ppp) cc_final: 0.7026 (pp-130) outliers start: 43 outliers final: 19 residues processed: 142 average time/residue: 1.7296 time to fit residues: 264.6177 Evaluate side-chains 127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 414 ARG Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 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 = 0.3816 r_free = 0.3816 target = 0.129072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078919 restraints weight = 17351.398| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.89 r_work: 0.2883 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 9572 Z= 0.338 Angle : 0.644 8.856 12983 Z= 0.338 Chirality : 0.044 0.170 1442 Planarity : 0.004 0.036 1654 Dihedral : 6.271 59.875 1331 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 5.02 % Allowed : 25.58 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.42 (0.25), residues: 1164 helix: 1.37 (0.26), residues: 446 sheet: -0.06 (0.39), residues: 194 loop : -1.90 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.004 0.001 HIS R 171 PHE 0.022 0.002 PHE N 108 TYR 0.021 0.002 TYR R 148 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 GLN cc_start: 0.7717 (mp10) cc_final: 0.7350 (pt0) REVERT: R 263 GLN cc_start: 0.7735 (pm20) cc_final: 0.7114 (tm-30) REVERT: R 348 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8229 (tpm-80) REVERT: A 18 MET cc_start: 0.9111 (tpp) cc_final: 0.8882 (ttm) REVERT: A 231 ASN cc_start: 0.9514 (t0) cc_final: 0.9173 (m110) REVERT: A 284 ARG cc_start: 0.8689 (mpp80) cc_final: 0.8470 (mpt-90) REVERT: A 359 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8721 (mp0) REVERT: P 21 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.8905 (t0) REVERT: B 9 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: B 172 GLU cc_start: 0.9437 (tp30) cc_final: 0.9167 (tp30) REVERT: B 175 GLN cc_start: 0.8714 (mp10) cc_final: 0.8222 (mp10) REVERT: B 217 MET cc_start: 0.8112 (pmm) cc_final: 0.7823 (pmm) REVERT: G 21 MET cc_start: 0.7290 (ppp) cc_final: 0.7075 (pp-130) outliers start: 50 outliers final: 25 residues processed: 148 average time/residue: 1.2270 time to fit residues: 194.5924 Evaluate side-chains 127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.080230 restraints weight = 17514.128| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.94 r_work: 0.2908 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9572 Z= 0.257 Angle : 0.622 8.838 12983 Z= 0.323 Chirality : 0.042 0.153 1442 Planarity : 0.003 0.035 1654 Dihedral : 5.967 58.752 1331 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.01 % Allowed : 27.08 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.30 (0.25), residues: 1164 helix: 1.48 (0.26), residues: 450 sheet: -0.13 (0.39), residues: 203 loop : -1.82 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 39 HIS 0.005 0.001 HIS R 171 PHE 0.015 0.001 PHE R 156 TYR 0.019 0.001 TYR R 148 ARG 0.008 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 348 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8128 (tpm-80) REVERT: A 18 MET cc_start: 0.9127 (tpp) cc_final: 0.8881 (ttm) REVERT: A 53 MET cc_start: 0.8969 (mmm) cc_final: 0.8659 (mpp) REVERT: A 231 ASN cc_start: 0.9502 (t0) cc_final: 0.9176 (m110) REVERT: A 284 ARG cc_start: 0.8698 (mpp80) cc_final: 0.8439 (mpt-90) REVERT: P 21 ASP cc_start: 0.9268 (m-30) cc_final: 0.8923 (t0) REVERT: B 9 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: B 172 GLU cc_start: 0.9421 (tp30) cc_final: 0.9154 (tp30) REVERT: B 175 GLN cc_start: 0.8711 (mp10) cc_final: 0.8161 (mp10) REVERT: B 217 MET cc_start: 0.8190 (pmm) cc_final: 0.7940 (pmm) REVERT: B 260 GLU cc_start: 0.8417 (pp20) cc_final: 0.7931 (pp20) REVERT: G 21 MET cc_start: 0.7305 (ppp) cc_final: 0.7094 (pp-130) outliers start: 40 outliers final: 26 residues processed: 139 average time/residue: 1.2152 time to fit residues: 180.8238 Evaluate side-chains 130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 406 ASN A 43 ASN N 39 GLN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082905 restraints weight = 17606.467| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.96 r_work: 0.2952 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 9572 Z= 0.216 Angle : 0.615 9.974 12983 Z= 0.316 Chirality : 0.041 0.149 1442 Planarity : 0.004 0.071 1654 Dihedral : 5.662 56.878 1331 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.21 % Allowed : 28.59 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.03 (0.25), residues: 1164 helix: 1.71 (0.26), residues: 448 sheet: 0.43 (0.42), residues: 182 loop : -1.79 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.005 0.000 HIS R 171 PHE 0.015 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.012 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: R 43 ARG cc_start: 0.8930 (tmm160) cc_final: 0.8652 (ptp90) REVERT: R 102 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6521 (mpp-170) REVERT: R 110 TRP cc_start: 0.2866 (OUTLIER) cc_final: 0.1941 (m100) REVERT: R 348 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8095 (tpm-80) REVERT: A 18 MET cc_start: 0.9089 (tpp) cc_final: 0.8877 (ttm) REVERT: A 231 ASN cc_start: 0.9465 (t0) cc_final: 0.9167 (m110) REVERT: A 284 ARG cc_start: 0.8672 (mpp80) cc_final: 0.8388 (mpt-90) REVERT: A 359 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8698 (mp0) REVERT: P 21 ASP cc_start: 0.9327 (m-30) cc_final: 0.8958 (t0) REVERT: B 9 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: B 172 GLU cc_start: 0.9391 (tp30) cc_final: 0.9118 (tp30) REVERT: B 175 GLN cc_start: 0.8727 (mp10) cc_final: 0.8205 (mp10) REVERT: B 217 MET cc_start: 0.8187 (pmm) cc_final: 0.7954 (pmm) REVERT: B 259 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: G 21 MET cc_start: 0.7319 (ppp) cc_final: 0.7078 (pp-130) REVERT: G 54 VAL cc_start: 0.8244 (p) cc_final: 0.7978 (p) REVERT: N 47 TRP cc_start: 0.7171 (t60) cc_final: 0.6922 (t60) outliers start: 32 outliers final: 16 residues processed: 139 average time/residue: 1.3487 time to fit residues: 199.6895 Evaluate side-chains 124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 406 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079918 restraints weight = 17443.177| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.93 r_work: 0.2903 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9572 Z= 0.300 Angle : 0.673 12.759 12983 Z= 0.347 Chirality : 0.043 0.154 1442 Planarity : 0.004 0.086 1654 Dihedral : 5.620 59.789 1326 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.71 % Allowed : 29.79 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.03 (0.25), residues: 1164 helix: 1.69 (0.26), residues: 450 sheet: 0.37 (0.40), residues: 194 loop : -1.80 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.019 0.002 PHE N 108 TYR 0.020 0.001 TYR R 148 ARG 0.014 0.001 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: R 43 ARG cc_start: 0.8921 (tmm160) cc_final: 0.8557 (mtm180) REVERT: R 110 TRP cc_start: 0.3039 (OUTLIER) cc_final: 0.2193 (m100) REVERT: R 348 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8154 (tpm-80) REVERT: A 18 MET cc_start: 0.9118 (tpp) cc_final: 0.8888 (ttm) REVERT: A 231 ASN cc_start: 0.9481 (t0) cc_final: 0.9169 (m110) REVERT: A 284 ARG cc_start: 0.8689 (mpp80) cc_final: 0.8383 (mpt-90) REVERT: P 21 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.8985 (t0) REVERT: B 9 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: B 172 GLU cc_start: 0.9417 (tp30) cc_final: 0.9151 (tp30) REVERT: B 175 GLN cc_start: 0.8739 (mp10) cc_final: 0.8211 (mp10) REVERT: B 217 MET cc_start: 0.8315 (pmm) cc_final: 0.8034 (pmm) REVERT: B 260 GLU cc_start: 0.8731 (pm20) cc_final: 0.8502 (pm20) REVERT: G 21 MET cc_start: 0.7357 (ppp) cc_final: 0.7112 (pp-130) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 1.5477 time to fit residues: 208.0631 Evaluate side-chains 122 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 60 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081222 restraints weight = 17540.814| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.93 r_work: 0.2923 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9572 Z= 0.236 Angle : 0.659 12.001 12983 Z= 0.339 Chirality : 0.042 0.153 1442 Planarity : 0.004 0.077 1654 Dihedral : 5.369 59.382 1322 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.71 % Allowed : 29.89 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.05 (0.25), residues: 1164 helix: 1.80 (0.26), residues: 449 sheet: 0.39 (0.40), residues: 194 loop : -1.78 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.014 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.012 0.001 ARG P 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: R 43 ARG cc_start: 0.8925 (tmm160) cc_final: 0.8597 (mtm180) REVERT: R 346 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6039 (mmpt) REVERT: R 348 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8163 (tpm-80) REVERT: A 18 MET cc_start: 0.9102 (tpp) cc_final: 0.8891 (ttm) REVERT: A 53 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8952 (mpp) REVERT: A 231 ASN cc_start: 0.9480 (t0) cc_final: 0.9184 (m110) REVERT: A 284 ARG cc_start: 0.8678 (mpp80) cc_final: 0.8369 (mpt-90) REVERT: P 21 ASP cc_start: 0.9342 (OUTLIER) cc_final: 0.9000 (t0) REVERT: P 26 LEU cc_start: 0.8742 (tp) cc_final: 0.8489 (tt) REVERT: B 9 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: B 172 GLU cc_start: 0.9402 (tp30) cc_final: 0.9131 (tp30) REVERT: B 175 GLN cc_start: 0.8748 (mp10) cc_final: 0.8262 (mp10) REVERT: B 217 MET cc_start: 0.8364 (pmm) cc_final: 0.8042 (pmm) REVERT: G 21 MET cc_start: 0.7365 (ppp) cc_final: 0.7118 (pp-130) REVERT: N 47 TRP cc_start: 0.7397 (t60) cc_final: 0.7119 (t60) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 1.3374 time to fit residues: 178.6136 Evaluate side-chains 124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079966 restraints weight = 17507.227| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.94 r_work: 0.2905 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9572 Z= 0.279 Angle : 0.676 12.990 12983 Z= 0.351 Chirality : 0.042 0.156 1442 Planarity : 0.004 0.064 1654 Dihedral : 5.232 58.350 1320 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.81 % Allowed : 29.99 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.01 (0.25), residues: 1164 helix: 1.78 (0.26), residues: 449 sheet: 0.32 (0.40), residues: 194 loop : -1.80 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 110 HIS 0.006 0.001 HIS R 171 PHE 0.018 0.001 PHE N 108 TYR 0.020 0.001 TYR R 148 ARG 0.012 0.001 ARG P 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8637.85 seconds wall clock time: 153 minutes 27.55 seconds (9207.55 seconds total)