Starting phenix.real_space_refine on Wed Apr 30 12:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jip_36323/04_2025/8jip_36323_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jip_36323/04_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_36323/04_2025/8jip_36323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jip_36323/04_2025/8jip_36323.map" model { file = "/net/cci-nas-00/data/ceres_data/8jip_36323/04_2025/8jip_36323_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jip_36323/04_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.51, per 1000 atoms: 0.59 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 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: 0.99 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: 2.34 Time building geometry restraints manager: 2.91 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: 0.980 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- 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 : 0.007 0.279 9579 Z= 0.525 Angle : 1.049 12.753 12995 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 Details of bonding type rmsd hydrogen bonds : bond 0.27550 ( 366) hydrogen bonds : angle 8.75095 ( 1044) SS BOND : bond 0.00225 ( 6) SS BOND : angle 1.19110 ( 12) covalent geometry : bond 0.00625 ( 9572) covalent geometry : angle 1.04898 (12983) Misc. bond : bond 0.27876 ( 1) *********************** 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 : 1.060 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: 1.3307 time to fit residues: 402.6182 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 : 1.058 ------------------------------------------------------------------------------- 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 9579 Z= 0.193 Angle : 0.701 8.888 12995 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 Details of bonding type rmsd hydrogen bonds : bond 0.06482 ( 366) hydrogen bonds : angle 5.02182 ( 1044) SS BOND : bond 0.00171 ( 6) SS BOND : angle 1.28213 ( 12) covalent geometry : bond 0.00446 ( 9572) covalent geometry : angle 0.70042 (12983) Misc. bond : bond 0.00090 ( 1) *********************** 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 : 1.401 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: 1.6048 time to fit residues: 284.6225 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 : 1.404 ------------------------------------------------------------------------------- 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: 0.9980 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: 3.3998 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.127918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077662 restraints weight = 17573.268| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.93 r_work: 0.2855 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9579 Z= 0.300 Angle : 0.733 8.585 12995 Z= 0.388 Chirality : 0.047 0.205 1442 Planarity : 0.005 0.039 1654 Dihedral : 8.052 56.983 1353 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 5.82 % Allowed : 22.07 % Favored : 72.12 % 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 0.017 0.002 TRP N 36 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE N 108 TYR 0.023 0.002 TYR N 80 ARG 0.013 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.07232 ( 366) hydrogen bonds : angle 4.79987 ( 1044) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.37707 ( 12) covalent geometry : bond 0.00708 ( 9572) covalent geometry : angle 0.73247 (12983) Misc. bond : bond 0.00079 ( 1) *********************** 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 168 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 110 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: R 102 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6064 (mpp-170) REVERT: R 263 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6927 (tm-30) REVERT: R 348 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8182 (tpm-80) REVERT: R 414 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7727 (ttm110) REVERT: R 415 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7796 (mtmm) REVERT: A 231 ASN cc_start: 0.9534 (t0) cc_final: 0.9284 (t0) REVERT: B 172 GLU cc_start: 0.9443 (tp30) cc_final: 0.9176 (tp30) REVERT: B 175 GLN cc_start: 0.8665 (mp10) cc_final: 0.8180 (mp10) REVERT: B 217 MET cc_start: 0.8037 (pmm) cc_final: 0.7794 (pmm) REVERT: B 260 GLU cc_start: 0.8340 (pp20) cc_final: 0.8063 (pp20) REVERT: G 21 MET cc_start: 0.7303 (ppp) cc_final: 0.7066 (pp-130) outliers start: 58 outliers final: 30 residues processed: 156 average time/residue: 1.1742 time to fit residues: 196.6262 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 : 1.047 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 0.0010 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.133254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083088 restraints weight = 17421.399| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.98 r_work: 0.2966 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9579 Z= 0.120 Angle : 0.597 10.487 12995 Z= 0.308 Chirality : 0.041 0.168 1442 Planarity : 0.004 0.038 1654 Dihedral : 7.038 58.822 1339 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 3.11 % Allowed : 25.48 % Favored : 71.41 % 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: -0.52 (0.25), residues: 1164 helix: 1.12 (0.26), residues: 448 sheet: 0.30 (0.41), residues: 180 loop : -1.92 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.003 0.001 HIS R 171 PHE 0.018 0.001 PHE R 156 TYR 0.016 0.001 TYR R 148 ARG 0.016 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 366) hydrogen bonds : angle 4.14201 ( 1044) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.65925 ( 12) covalent geometry : bond 0.00282 ( 9572) covalent geometry : angle 0.59661 (12983) Misc. bond : bond 0.00004 ( 1) *********************** 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 150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 224 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8747 (tm) REVERT: R 348 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8104 (tpm-80) REVERT: A 18 MET cc_start: 0.9116 (tpp) cc_final: 0.8901 (ttm) REVERT: A 52 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 53 MET cc_start: 0.8942 (mmm) cc_final: 0.8617 (mpp) REVERT: A 231 ASN cc_start: 0.9485 (t0) cc_final: 0.9138 (m110) REVERT: A 284 ARG cc_start: 0.8670 (mpp80) cc_final: 0.8441 (mpt-90) REVERT: B 172 GLU cc_start: 0.9407 (tp30) cc_final: 0.9110 (tp30) REVERT: B 175 GLN cc_start: 0.8692 (mp10) cc_final: 0.8176 (mp10) REVERT: B 217 MET cc_start: 0.7984 (pmm) cc_final: 0.7759 (pmm) REVERT: G 21 MET cc_start: 0.7225 (ppp) cc_final: 0.6970 (pp-130) outliers start: 31 outliers final: 13 residues processed: 146 average time/residue: 1.1555 time to fit residues: 180.9979 Evaluate side-chains 120 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 52 optimal weight: 0.0000 chunk 94 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 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 = 0.3860 r_free = 0.3860 target = 0.132563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.082504 restraints weight = 17407.407| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.95 r_work: 0.2955 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9579 Z= 0.129 Angle : 0.596 9.463 12995 Z= 0.307 Chirality : 0.042 0.215 1442 Planarity : 0.003 0.043 1654 Dihedral : 6.392 57.585 1331 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 3.91 % Allowed : 25.68 % Favored : 70.41 % 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: -0.24 (0.25), residues: 1164 helix: 1.43 (0.26), residues: 447 sheet: 0.28 (0.41), residues: 189 loop : -1.80 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.003 0.000 HIS R 171 PHE 0.015 0.001 PHE R 156 TYR 0.018 0.001 TYR R 148 ARG 0.012 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 366) hydrogen bonds : angle 3.96034 ( 1044) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.65509 ( 12) covalent geometry : bond 0.00304 ( 9572) covalent geometry : angle 0.59606 (12983) Misc. bond : bond 0.00012 ( 1) *********************** 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 146 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 224 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8599 (tm) REVERT: R 228 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (mt) REVERT: R 263 GLN cc_start: 0.7723 (pm20) cc_final: 0.7212 (tm130) REVERT: R 348 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8136 (tpm-80) REVERT: R 415 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7758 (mtmm) REVERT: A 18 MET cc_start: 0.9138 (tpp) cc_final: 0.8896 (ttm) REVERT: A 20 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8222 (tm-30) REVERT: A 231 ASN cc_start: 0.9480 (t0) cc_final: 0.9163 (m110) REVERT: A 284 ARG cc_start: 0.8677 (mpp80) cc_final: 0.8421 (mpt-90) REVERT: B 9 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 172 GLU cc_start: 0.9419 (tp30) cc_final: 0.9136 (tp30) REVERT: B 175 GLN cc_start: 0.8719 (mp10) cc_final: 0.8183 (mp10) REVERT: B 217 MET cc_start: 0.8062 (pmm) cc_final: 0.7849 (pmm) REVERT: G 21 MET cc_start: 0.7246 (ppp) cc_final: 0.6996 (pp-130) outliers start: 39 outliers final: 17 residues processed: 137 average time/residue: 1.2011 time to fit residues: 176.5840 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 : 1.052 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082255 restraints weight = 17288.366| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.83 r_work: 0.2936 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9579 Z= 0.158 Angle : 0.608 9.056 12995 Z= 0.315 Chirality : 0.042 0.170 1442 Planarity : 0.003 0.036 1654 Dihedral : 6.215 57.779 1330 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.01 % Allowed : 25.78 % Favored : 70.21 % 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: -0.18 (0.25), residues: 1164 helix: 1.53 (0.26), residues: 446 sheet: 0.23 (0.40), residues: 191 loop : -1.79 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 39 HIS 0.004 0.001 HIS R 171 PHE 0.016 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.011 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 366) hydrogen bonds : angle 3.91850 ( 1044) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.70326 ( 12) covalent geometry : bond 0.00384 ( 9572) covalent geometry : angle 0.60778 (12983) Misc. bond : bond 0.00031 ( 1) *********************** 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 144 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 GLN cc_start: 0.7772 (mp10) cc_final: 0.7284 (pt0) REVERT: R 224 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8608 (tm) REVERT: R 263 GLN cc_start: 0.7737 (pm20) cc_final: 0.7090 (tm-30) REVERT: R 348 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (tpm-80) REVERT: R 415 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7771 (mtmm) REVERT: A 18 MET cc_start: 0.9116 (tpp) cc_final: 0.8878 (ttm) REVERT: A 231 ASN cc_start: 0.9482 (t0) cc_final: 0.9161 (m110) REVERT: A 284 ARG cc_start: 0.8676 (mpp80) cc_final: 0.8391 (mpt-90) REVERT: A 359 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8780 (mp0) REVERT: P 21 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.8941 (t0) REVERT: B 9 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: B 172 GLU cc_start: 0.9418 (tp30) cc_final: 0.9131 (tp30) REVERT: B 175 GLN cc_start: 0.8720 (mp10) cc_final: 0.8184 (mp10) REVERT: B 217 MET cc_start: 0.8074 (pmm) cc_final: 0.7866 (pmm) REVERT: B 260 GLU cc_start: 0.8238 (pp20) cc_final: 0.7973 (pp20) REVERT: G 21 MET cc_start: 0.7248 (ppp) cc_final: 0.7002 (pp-130) outliers start: 40 outliers final: 21 residues processed: 137 average time/residue: 1.3364 time to fit residues: 196.6081 Evaluate side-chains 123 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 224 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 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 16 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 300 LEU Chi-restraints excluded: chain N residue 19 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083655 restraints weight = 17374.598| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.91 r_work: 0.2965 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9579 Z= 0.115 Angle : 0.587 11.513 12995 Z= 0.300 Chirality : 0.041 0.150 1442 Planarity : 0.003 0.035 1654 Dihedral : 5.855 59.002 1330 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.91 % Allowed : 27.68 % 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: -0.02 (0.25), residues: 1164 helix: 1.69 (0.26), residues: 447 sheet: 0.48 (0.42), residues: 182 loop : -1.77 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 39 HIS 0.005 0.001 HIS R 171 PHE 0.014 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.009 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 366) hydrogen bonds : angle 3.74620 ( 1044) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.60904 ( 12) covalent geometry : bond 0.00277 ( 9572) covalent geometry : angle 0.58686 (12983) Misc. bond : bond 0.00001 ( 1) *********************** 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 139 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6150 (ptt-90) REVERT: R 224 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (tm) REVERT: R 263 GLN cc_start: 0.7696 (pm20) cc_final: 0.6950 (tm-30) REVERT: R 348 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (tpm-80) REVERT: R 415 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7715 (mtmm) REVERT: A 18 MET cc_start: 0.9124 (tpp) cc_final: 0.8869 (ttm) REVERT: A 231 ASN cc_start: 0.9468 (t0) cc_final: 0.9165 (m110) REVERT: A 284 ARG cc_start: 0.8669 (mpp80) cc_final: 0.8316 (mpt-90) REVERT: A 359 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8762 (mp0) REVERT: P 21 ASP cc_start: 0.9250 (m-30) cc_final: 0.8951 (t0) REVERT: B 9 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: B 172 GLU cc_start: 0.9404 (tp30) cc_final: 0.9120 (tp30) REVERT: B 175 GLN cc_start: 0.8701 (mp10) cc_final: 0.8172 (mp10) REVERT: B 217 MET cc_start: 0.8089 (pmm) cc_final: 0.7835 (pmm) REVERT: B 259 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: G 21 MET cc_start: 0.7271 (ppp) cc_final: 0.7036 (pp-130) REVERT: N 47 TRP cc_start: 0.7166 (t60) cc_final: 0.6950 (t60) outliers start: 29 outliers final: 16 residues processed: 131 average time/residue: 1.7997 time to fit residues: 250.8017 Evaluate side-chains 126 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 232 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 389 SER Chi-restraints excluded: chain A residue 50 VAL 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 79 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083729 restraints weight = 17664.923| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.98 r_work: 0.2971 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 9579 Z= 0.116 Angle : 0.599 11.542 12995 Z= 0.306 Chirality : 0.040 0.146 1442 Planarity : 0.004 0.082 1654 Dihedral : 5.639 59.739 1330 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.21 % Allowed : 27.88 % 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: 0.10 (0.25), residues: 1164 helix: 1.82 (0.26), residues: 447 sheet: 0.56 (0.42), residues: 182 loop : -1.74 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.004 0.000 HIS R 171 PHE 0.013 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.009 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 366) hydrogen bonds : angle 3.65818 ( 1044) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.60711 ( 12) covalent geometry : bond 0.00293 ( 9572) covalent geometry : angle 0.59903 (12983) Misc. bond : bond 0.00001 ( 1) *********************** 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 139 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5841 (ptt-90) REVERT: R 224 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8428 (tm) REVERT: R 263 GLN cc_start: 0.7690 (pm20) cc_final: 0.6918 (tm-30) REVERT: R 348 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8162 (tpm-80) REVERT: R 415 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7714 (mtmm) REVERT: A 18 MET cc_start: 0.9107 (tpp) cc_final: 0.8868 (ttm) REVERT: A 231 ASN cc_start: 0.9454 (t0) cc_final: 0.9167 (m110) REVERT: A 284 ARG cc_start: 0.8665 (mpp80) cc_final: 0.8310 (mpt-90) REVERT: A 359 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8769 (mp0) REVERT: P 21 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8983 (t0) REVERT: B 9 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: B 172 GLU cc_start: 0.9396 (tp30) cc_final: 0.9111 (tp30) REVERT: B 175 GLN cc_start: 0.8736 (mp10) cc_final: 0.8227 (mp10) REVERT: B 217 MET cc_start: 0.8068 (pmm) cc_final: 0.7857 (pmm) REVERT: G 21 MET cc_start: 0.7271 (ppp) cc_final: 0.7038 (pp-130) REVERT: N 47 TRP cc_start: 0.7117 (t60) cc_final: 0.6898 (t60) outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 1.2761 time to fit residues: 178.8621 Evaluate side-chains 125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 224 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 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 P residue 21 ASP Chi-restraints excluded: chain B residue 9 GLN 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 300 LEU Chi-restraints excluded: chain G residue 50 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: 1.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081678 restraints weight = 17396.401| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.93 r_work: 0.2936 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9579 Z= 0.149 Angle : 0.634 12.518 12995 Z= 0.328 Chirality : 0.042 0.149 1442 Planarity : 0.004 0.063 1654 Dihedral : 5.600 59.683 1329 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.11 % Allowed : 27.88 % Favored : 69.01 % 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: 0.06 (0.25), residues: 1164 helix: 1.85 (0.26), residues: 449 sheet: 0.24 (0.40), residues: 196 loop : -1.76 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 110 HIS 0.005 0.001 HIS R 171 PHE 0.016 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.009 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 366) hydrogen bonds : angle 3.70440 ( 1044) SS BOND : bond 0.00174 ( 6) SS BOND : angle 0.79642 ( 12) covalent geometry : bond 0.00364 ( 9572) covalent geometry : angle 0.63404 (12983) Misc. bond : bond 0.00020 ( 1) *********************** 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 136 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: R 43 ARG cc_start: 0.8933 (tmm160) cc_final: 0.8668 (ptp-170) REVERT: R 224 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8401 (tm) REVERT: R 348 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (tpm-80) REVERT: A 18 MET cc_start: 0.9112 (tpp) cc_final: 0.8876 (ttm) REVERT: A 231 ASN cc_start: 0.9471 (t0) cc_final: 0.9172 (m110) REVERT: A 284 ARG cc_start: 0.8656 (mpp80) cc_final: 0.8304 (mpt-90) REVERT: P 21 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8907 (t0) REVERT: B 9 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: B 172 GLU cc_start: 0.9408 (tp30) cc_final: 0.9128 (tp30) REVERT: B 175 GLN cc_start: 0.8747 (mp10) cc_final: 0.8243 (mp10) REVERT: G 21 MET cc_start: 0.7268 (ppp) cc_final: 0.7037 (pp-130) REVERT: G 47 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7866 (mm-30) REVERT: N 47 TRP cc_start: 0.7397 (t60) cc_final: 0.7129 (t60) outliers start: 31 outliers final: 19 residues processed: 131 average time/residue: 1.5248 time to fit residues: 213.7359 Evaluate side-chains 124 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 311 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 R residue 405 VAL 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 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 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: 0.9990 chunk 107 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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** A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.132485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082714 restraints weight = 17493.065| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.96 r_work: 0.2950 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 9579 Z= 0.135 Angle : 0.651 12.641 12995 Z= 0.333 Chirality : 0.041 0.148 1442 Planarity : 0.004 0.092 1654 Dihedral : 5.212 59.884 1322 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.81 % Allowed : 28.79 % Favored : 68.41 % 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: 0.14 (0.25), residues: 1164 helix: 1.92 (0.26), residues: 447 sheet: 0.36 (0.41), residues: 192 loop : -1.72 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.014 0.001 PHE G 61 TYR 0.018 0.001 TYR R 148 ARG 0.014 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 366) hydrogen bonds : angle 3.64606 ( 1044) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.71578 ( 12) covalent geometry : bond 0.00345 ( 9572) covalent geometry : angle 0.65111 (12983) Misc. bond : bond 0.00005 ( 1) ********************** 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 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 43 ARG cc_start: 0.8915 (tmm160) cc_final: 0.8570 (mtm180) REVERT: R 224 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8337 (tm) REVERT: R 263 GLN cc_start: 0.7673 (pm20) cc_final: 0.6549 (tp-100) REVERT: R 348 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8146 (tpm-80) REVERT: A 18 MET cc_start: 0.9100 (tpp) cc_final: 0.8872 (ttm) REVERT: A 231 ASN cc_start: 0.9465 (t0) cc_final: 0.9179 (m110) REVERT: A 359 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8664 (mp0) REVERT: P 21 ASP cc_start: 0.9309 (OUTLIER) cc_final: 0.8971 (t0) REVERT: B 9 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: B 172 GLU cc_start: 0.9399 (tp30) cc_final: 0.9115 (tp30) REVERT: B 175 GLN cc_start: 0.8739 (mp10) cc_final: 0.8238 (mp10) REVERT: B 217 MET cc_start: 0.8360 (pmm) cc_final: 0.8112 (pmm) REVERT: G 21 MET cc_start: 0.7239 (ppp) cc_final: 0.6998 (pp-130) REVERT: N 47 TRP cc_start: 0.7211 (t60) cc_final: 0.6967 (t60) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 1.3049 time to fit residues: 176.9879 Evaluate side-chains 128 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 224 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 R residue 405 VAL 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 152 LEU 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 53 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.133565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084275 restraints weight = 17411.402| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.90 r_work: 0.2975 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9579 Z= 0.124 Angle : 0.644 12.493 12995 Z= 0.329 Chirality : 0.041 0.147 1442 Planarity : 0.004 0.086 1654 Dihedral : 4.916 58.188 1320 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.31 % Allowed : 29.09 % Favored : 68.61 % 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: 0.20 (0.25), residues: 1164 helix: 2.01 (0.26), residues: 447 sheet: 0.34 (0.41), residues: 187 loop : -1.69 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.013 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.012 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 366) hydrogen bonds : angle 3.56125 ( 1044) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.65891 ( 12) covalent geometry : bond 0.00309 ( 9572) covalent geometry : angle 0.64353 (12983) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9274.24 seconds wall clock time: 163 minutes 32.17 seconds (9812.17 seconds total)