Starting phenix.real_space_refine on Tue Apr 29 11:38:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339.map" model { file = "/net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n4b_0339/04_2025/6n4b_0339_neut.cif" } resolution = 3.0 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= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5423 2.51 5 N 1457 2.21 5 O 1514 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8453 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1988 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'CLR': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.35, per 1000 atoms: 0.63 Number of scatterers: 8453 At special positions: 0 Unit cell: (109.22, 122.98, 109.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 1 9.00 O 1514 8.00 N 1457 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.718A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.937A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.453A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 4.060A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.911A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.665A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.509A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.577A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.506A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.550A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.803A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.622A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'R' and resid 112 through 143 removed outlier: 4.519A pdb=" N VAL R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 179 removed outlier: 3.937A pdb=" N PHE R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 179 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 191 removed outlier: 4.288A pdb=" N LEU R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE R 191 " --> pdb=" O ASN R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 3.622A pdb=" N ILE R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 220 removed outlier: 3.632A pdb=" N ILE R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 228 removed outlier: 4.523A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 249 Processing helix chain 'R' and resid 249 through 254 removed outlier: 4.183A pdb=" N LEU R 253 " --> pdb=" O VAL R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 277 Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.693A pdb=" N VAL R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 355 removed outlier: 3.842A pdb=" N ALA R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 363 Processing helix chain 'R' and resid 374 through 399 removed outlier: 3.708A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 388 " --> pdb=" O MET R 384 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 410 removed outlier: 3.514A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.707A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.273A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.601A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.918A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.568A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.012A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.730A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.765A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.660A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.100A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.658A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 936 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: 2.26 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1206 1.24 - 1.39: 2297 1.39 - 1.53: 4598 1.53 - 1.67: 451 1.67 - 1.81: 84 Bond restraints: 8636 Sorted by residual: bond pdb=" CAT KCA R 501 " pdb=" FAU KCA R 501 " ideal model delta sigma weight residual 1.342 1.101 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" CAB KCA R 501 " pdb=" CAM KCA R 501 " ideal model delta sigma weight residual 1.476 1.351 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CA TRP B 339 " pdb=" C TRP B 339 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.18e-02 7.18e+03 3.19e+01 bond pdb=" CAP KCA R 501 " pdb=" CAQ KCA R 501 " ideal model delta sigma weight residual 1.507 1.395 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.19e-02 7.06e+03 2.07e+01 ... (remaining 8631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 11350 3.46 - 6.92: 352 6.92 - 10.39: 39 10.39 - 13.85: 6 13.85 - 17.31: 1 Bond angle restraints: 11748 Sorted by residual: angle pdb=" N PHE R 177 " pdb=" CA PHE R 177 " pdb=" C PHE R 177 " ideal model delta sigma weight residual 111.14 123.07 -11.93 1.08e+00 8.57e-01 1.22e+02 angle pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 120.60 137.91 -17.31 2.20e+00 2.07e-01 6.19e+01 angle pdb=" N TYR R 397 " pdb=" CA TYR R 397 " pdb=" C TYR R 397 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LEU R 193 " pdb=" CA LEU R 193 " pdb=" C LEU R 193 " ideal model delta sigma weight residual 114.39 103.36 11.03 1.45e+00 4.76e-01 5.78e+01 angle pdb=" N LEU S 225 " pdb=" CA LEU S 225 " pdb=" C LEU S 225 " ideal model delta sigma weight residual 111.17 121.84 -10.67 1.41e+00 5.03e-01 5.73e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4939 17.03 - 34.07: 177 34.07 - 51.10: 34 51.10 - 68.14: 9 68.14 - 85.17: 2 Dihedral angle restraints: 5161 sinusoidal: 1911 harmonic: 3250 Sorted by residual: dihedral pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual 122.80 143.79 -20.99 0 2.50e+00 1.60e-01 7.05e+01 dihedral pdb=" C TYR S 178 " pdb=" N TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual -122.60 -142.31 19.71 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" C TRP R 241 " pdb=" N TRP R 241 " pdb=" CA TRP R 241 " pdb=" CB TRP R 241 " ideal model delta harmonic sigma weight residual -122.60 -139.20 16.60 0 2.50e+00 1.60e-01 4.41e+01 ... (remaining 5158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1319 0.187 - 0.374: 42 0.374 - 0.561: 7 0.561 - 0.749: 1 0.749 - 0.936: 1 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CA TRP R 241 " pdb=" N TRP R 241 " pdb=" C TRP R 241 " pdb=" CB TRP R 241 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA LEU S 225 " pdb=" N LEU S 225 " pdb=" C LEU S 225 " pdb=" CB LEU S 225 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 ... (remaining 1367 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.032 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP S 111 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 394 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C PRO R 394 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO R 394 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE R 395 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 256 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" CG ASN A 256 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 256 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 51 2.46 - 3.07: 5955 3.07 - 3.68: 11467 3.68 - 4.29: 16674 4.29 - 4.90: 28813 Nonbonded interactions: 62960 Sorted by model distance: nonbonded pdb=" CE MET R 371 " pdb=" CB ILE R 375 " model vdw 1.855 3.890 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 1.962 3.040 nonbonded pdb=" O ASP B 38 " pdb=" OD1 ASP B 38 " model vdw 1.981 3.040 nonbonded pdb=" O HIS S 220 " pdb=" ND1 HIS S 220 " model vdw 2.011 3.120 nonbonded pdb=" CD1 ILE S 126 " pdb=" OE2 GLU S 222 " model vdw 2.077 3.460 ... (remaining 62955 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: 0.910 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.690 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.568 8638 Z= 0.859 Angle : 1.400 17.310 11750 Z= 0.876 Chirality : 0.091 0.936 1370 Planarity : 0.008 0.075 1463 Dihedral : 9.763 85.169 3058 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 2.88 % Favored : 96.28 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.45 % 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 (0.23), residues: 1101 helix: -1.09 (0.27), residues: 320 sheet: -1.55 (0.30), residues: 253 loop : -1.65 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP S 111 HIS 0.011 0.003 HIS R 143 PHE 0.030 0.004 PHE A 196 TYR 0.049 0.005 TYR A 287 ARG 0.010 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.21552 ( 320) hydrogen bonds : angle 8.49648 ( 936) SS BOND : bond 0.00483 ( 1) SS BOND : angle 1.13652 ( 2) covalent geometry : bond 0.01127 ( 8636) covalent geometry : angle 1.40024 (11748) Misc. bond : bond 0.56806 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.818 Fit side-chains REVERT: A 14 GLU cc_start: 0.7919 (tt0) cc_final: 0.7571 (tt0) REVERT: B 13 GLN cc_start: 0.7174 (mt0) cc_final: 0.6929 (tt0) REVERT: C 18 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7065 (tp-100) REVERT: R 186 ARG cc_start: 0.6786 (mtm180) cc_final: 0.5387 (ttt180) REVERT: R 347 LEU cc_start: 0.8691 (tp) cc_final: 0.8428 (tt) outliers start: 7 outliers final: 4 residues processed: 229 average time/residue: 1.0543 time to fit residues: 258.3157 Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 264 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 255 ASN A 311 ASN B 91 HIS B 220 GLN B 259 GLN R 154 HIS R 178 HIS R 304 HIS S 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115432 restraints weight = 11755.648| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.94 r_work: 0.3536 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8638 Z= 0.169 Angle : 0.679 10.365 11750 Z= 0.359 Chirality : 0.045 0.168 1370 Planarity : 0.005 0.044 1463 Dihedral : 7.301 69.536 1359 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.84 % Allowed : 13.57 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.74 (0.24), residues: 1101 helix: -0.38 (0.28), residues: 344 sheet: -0.97 (0.29), residues: 272 loop : -1.75 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 332 HIS 0.006 0.001 HIS R 143 PHE 0.017 0.002 PHE R 289 TYR 0.024 0.002 TYR S 178 ARG 0.007 0.001 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 320) hydrogen bonds : angle 5.38298 ( 936) SS BOND : bond 0.00440 ( 1) SS BOND : angle 1.84721 ( 2) covalent geometry : bond 0.00381 ( 8636) covalent geometry : angle 0.67862 (11748) Misc. bond : bond 0.00294 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.874 Fit side-chains REVERT: A 333 GLN cc_start: 0.8376 (tp40) cc_final: 0.7721 (tm-30) REVERT: B 13 GLN cc_start: 0.6873 (mt0) cc_final: 0.6654 (tt0) REVERT: B 217 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8200 (pmm) REVERT: B 227 SER cc_start: 0.8863 (m) cc_final: 0.8165 (t) REVERT: B 292 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: C 18 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6725 (tp-100) REVERT: C 63 GLU cc_start: 0.6514 (tp30) cc_final: 0.6286 (tp30) REVERT: R 308 MET cc_start: 0.6678 (mmp) cc_final: 0.5757 (tmt) REVERT: R 309 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7450 (pt) REVERT: R 353 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7021 (tp) REVERT: S 60 TYR cc_start: 0.9149 (m-80) cc_final: 0.8948 (m-80) outliers start: 32 outliers final: 14 residues processed: 162 average time/residue: 0.9603 time to fit residues: 167.6480 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 113 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.147094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116813 restraints weight = 11934.347| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.95 r_work: 0.3523 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8638 Z= 0.112 Angle : 0.564 10.927 11750 Z= 0.296 Chirality : 0.042 0.213 1370 Planarity : 0.004 0.044 1463 Dihedral : 6.705 67.745 1355 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.72 % Allowed : 15.01 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.20 (0.24), residues: 1101 helix: 0.07 (0.29), residues: 350 sheet: -0.55 (0.30), residues: 272 loop : -1.53 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 143 PHE 0.012 0.001 PHE R 289 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 320) hydrogen bonds : angle 4.72513 ( 936) SS BOND : bond 0.00688 ( 1) SS BOND : angle 1.51986 ( 2) covalent geometry : bond 0.00240 ( 8636) covalent geometry : angle 0.56398 (11748) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.863 Fit side-chains REVERT: A 276 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8498 (pp20) REVERT: A 308 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 333 GLN cc_start: 0.8473 (tp40) cc_final: 0.7852 (tm-30) REVERT: B 217 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8306 (pmm) REVERT: B 227 SER cc_start: 0.8932 (m) cc_final: 0.8262 (t) REVERT: B 292 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: C 21 MET cc_start: 0.8392 (tpp) cc_final: 0.8140 (mpp) REVERT: C 58 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: C 63 GLU cc_start: 0.6693 (tp30) cc_final: 0.6370 (tp30) REVERT: R 308 MET cc_start: 0.6613 (mmp) cc_final: 0.5751 (tmt) REVERT: S 84 THR cc_start: 0.8149 (m) cc_final: 0.7791 (p) outliers start: 31 outliers final: 13 residues processed: 157 average time/residue: 0.9539 time to fit residues: 162.0762 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115583 restraints weight = 11903.320| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.96 r_work: 0.3503 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8638 Z= 0.116 Angle : 0.548 10.833 11750 Z= 0.288 Chirality : 0.041 0.223 1370 Planarity : 0.003 0.047 1463 Dihedral : 6.477 65.991 1354 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.96 % Allowed : 16.81 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.98 (0.25), residues: 1101 helix: 0.23 (0.29), residues: 356 sheet: -0.42 (0.30), residues: 278 loop : -1.43 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 279 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE A 189 TYR 0.017 0.001 TYR S 178 ARG 0.003 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 320) hydrogen bonds : angle 4.49072 ( 936) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.43795 ( 2) covalent geometry : bond 0.00261 ( 8636) covalent geometry : angle 0.54843 (11748) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.988 Fit side-chains REVERT: A 308 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 333 GLN cc_start: 0.8523 (tp40) cc_final: 0.7919 (tm-30) REVERT: B 217 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8320 (pmm) REVERT: B 227 SER cc_start: 0.8917 (m) cc_final: 0.8245 (t) REVERT: B 292 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: C 58 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: C 63 GLU cc_start: 0.6756 (tp30) cc_final: 0.6453 (tp30) REVERT: R 308 MET cc_start: 0.6613 (mmp) cc_final: 0.5780 (tmt) REVERT: R 353 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6978 (tp) REVERT: S 84 THR cc_start: 0.8151 (m) cc_final: 0.7782 (p) outliers start: 33 outliers final: 15 residues processed: 145 average time/residue: 1.0455 time to fit residues: 162.6898 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 0.0050 chunk 53 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118682 restraints weight = 11759.401| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.95 r_work: 0.3585 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8638 Z= 0.090 Angle : 0.513 12.055 11750 Z= 0.266 Chirality : 0.040 0.255 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.206 63.324 1354 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 17.53 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.66 (0.25), residues: 1101 helix: 0.56 (0.29), residues: 355 sheet: -0.27 (0.31), residues: 274 loop : -1.26 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 279 HIS 0.004 0.001 HIS R 143 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR S 95 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 320) hydrogen bonds : angle 4.24790 ( 936) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.36752 ( 2) covalent geometry : bond 0.00190 ( 8636) covalent geometry : angle 0.51286 (11748) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.975 Fit side-chains REVERT: A 46 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8185 (mttt) REVERT: A 308 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 333 GLN cc_start: 0.8425 (tp40) cc_final: 0.7818 (tm-30) REVERT: B 214 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8101 (mtt180) REVERT: B 217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8276 (pmm) REVERT: C 21 MET cc_start: 0.8369 (tpp) cc_final: 0.8025 (mpp) REVERT: C 58 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 63 GLU cc_start: 0.6406 (tp30) cc_final: 0.5957 (tp30) REVERT: R 308 MET cc_start: 0.6331 (mmp) cc_final: 0.5647 (tmt) REVERT: S 84 THR cc_start: 0.8046 (m) cc_final: 0.7763 (p) outliers start: 30 outliers final: 12 residues processed: 164 average time/residue: 0.9443 time to fit residues: 167.5377 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118919 restraints weight = 11722.025| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.87 r_work: 0.3517 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8638 Z= 0.123 Angle : 0.555 11.499 11750 Z= 0.290 Chirality : 0.041 0.250 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.179 62.941 1352 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.60 % Allowed : 19.57 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.54 (0.25), residues: 1101 helix: 0.69 (0.29), residues: 355 sheet: -0.20 (0.31), residues: 281 loop : -1.23 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 279 HIS 0.006 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR S 178 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 320) hydrogen bonds : angle 4.27735 ( 936) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.34027 ( 2) covalent geometry : bond 0.00283 ( 8636) covalent geometry : angle 0.55515 (11748) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8238 (mttp) REVERT: A 253 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7835 (tt) REVERT: A 308 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 333 GLN cc_start: 0.8492 (tp40) cc_final: 0.7871 (tm-30) REVERT: B 217 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8286 (pmm) REVERT: C 58 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: R 181 HIS cc_start: 0.7271 (t70) cc_final: 0.6009 (p90) REVERT: R 365 TYR cc_start: 0.7362 (t80) cc_final: 0.6978 (t80) REVERT: S 84 THR cc_start: 0.8133 (m) cc_final: 0.7770 (p) outliers start: 30 outliers final: 17 residues processed: 152 average time/residue: 0.9554 time to fit residues: 156.6302 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111481 restraints weight = 12035.283| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.87 r_work: 0.3455 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8638 Z= 0.161 Angle : 0.588 8.453 11750 Z= 0.310 Chirality : 0.043 0.198 1370 Planarity : 0.004 0.046 1463 Dihedral : 6.385 62.338 1352 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.96 % Allowed : 19.57 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1101 helix: 0.68 (0.29), residues: 357 sheet: -0.23 (0.30), residues: 282 loop : -1.31 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.021 0.002 PHE B 335 TYR 0.026 0.002 TYR S 178 ARG 0.010 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 320) hydrogen bonds : angle 4.49035 ( 936) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.46114 ( 2) covalent geometry : bond 0.00381 ( 8636) covalent geometry : angle 0.58783 (11748) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8275 (mttt) REVERT: A 308 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 316 THR cc_start: 0.8803 (m) cc_final: 0.8526 (p) REVERT: A 333 GLN cc_start: 0.8528 (tp40) cc_final: 0.7930 (tm-30) REVERT: B 217 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8228 (pmm) REVERT: C 11 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6392 (tm-30) REVERT: C 21 MET cc_start: 0.8430 (tpp) cc_final: 0.8164 (mpp) REVERT: C 32 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7273 (tttp) REVERT: C 58 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: S 84 THR cc_start: 0.8169 (m) cc_final: 0.7796 (p) REVERT: S 189 ASP cc_start: 0.7755 (t0) cc_final: 0.7334 (m-30) outliers start: 33 outliers final: 18 residues processed: 150 average time/residue: 1.1591 time to fit residues: 189.9688 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 0.0270 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109378 restraints weight = 11880.891| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.01 r_work: 0.3325 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8638 Z= 0.093 Angle : 0.539 13.240 11750 Z= 0.278 Chirality : 0.040 0.201 1370 Planarity : 0.003 0.043 1463 Dihedral : 5.832 59.684 1352 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.80 % Allowed : 21.97 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.29 (0.26), residues: 1101 helix: 0.90 (0.29), residues: 362 sheet: -0.01 (0.31), residues: 281 loop : -1.15 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 143 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR R 365 ARG 0.010 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 320) hydrogen bonds : angle 4.14859 ( 936) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.14991 ( 2) covalent geometry : bond 0.00195 ( 8636) covalent geometry : angle 0.53904 (11748) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.865 Fit side-chains REVERT: A 253 ILE cc_start: 0.8054 (tt) cc_final: 0.7795 (tp) REVERT: A 316 THR cc_start: 0.8839 (m) cc_final: 0.8582 (p) REVERT: A 333 GLN cc_start: 0.8630 (tp40) cc_final: 0.8044 (tm-30) REVERT: B 217 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8291 (pmm) REVERT: B 234 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: C 21 MET cc_start: 0.8484 (tpp) cc_final: 0.8147 (mpp) REVERT: C 58 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: R 365 TYR cc_start: 0.7437 (t80) cc_final: 0.7117 (t80) REVERT: S 84 THR cc_start: 0.8307 (m) cc_final: 0.8028 (p) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.9465 time to fit residues: 146.3379 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106714 restraints weight = 11905.298| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.01 r_work: 0.3288 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8638 Z= 0.120 Angle : 0.554 9.138 11750 Z= 0.289 Chirality : 0.041 0.216 1370 Planarity : 0.003 0.044 1463 Dihedral : 5.934 57.761 1352 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.16 % Allowed : 22.21 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.22 (0.26), residues: 1101 helix: 0.99 (0.29), residues: 362 sheet: -0.02 (0.31), residues: 289 loop : -1.13 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.022 0.001 PHE B 335 TYR 0.018 0.001 TYR S 178 ARG 0.009 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 320) hydrogen bonds : angle 4.19863 ( 936) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.27723 ( 2) covalent geometry : bond 0.00277 ( 8636) covalent geometry : angle 0.55381 (11748) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.747 Fit side-chains REVERT: A 253 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7902 (tp) REVERT: A 316 THR cc_start: 0.8850 (m) cc_final: 0.8589 (p) REVERT: A 333 GLN cc_start: 0.8622 (tp40) cc_final: 0.8007 (tm-30) REVERT: B 217 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8362 (pmm) REVERT: C 21 MET cc_start: 0.8477 (tpp) cc_final: 0.8212 (mpp) REVERT: C 32 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7353 (tttp) REVERT: C 58 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: R 365 TYR cc_start: 0.7418 (t80) cc_final: 0.7208 (t80) REVERT: S 84 THR cc_start: 0.8279 (m) cc_final: 0.7997 (p) REVERT: S 189 ASP cc_start: 0.7804 (t0) cc_final: 0.7364 (m-30) REVERT: S 206 ARG cc_start: 0.8111 (ppt90) cc_final: 0.7164 (ptm160) outliers start: 18 outliers final: 11 residues processed: 137 average time/residue: 1.0688 time to fit residues: 157.0881 Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3801 r_free = 0.3801 target = 0.137630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105212 restraints weight = 11831.137| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.00 r_work: 0.3267 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8638 Z= 0.141 Angle : 0.593 13.783 11750 Z= 0.305 Chirality : 0.042 0.217 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.017 57.503 1352 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.04 % Allowed : 22.33 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.23 (0.26), residues: 1101 helix: 1.10 (0.30), residues: 354 sheet: -0.12 (0.30), residues: 289 loop : -1.13 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.013 0.001 PHE B 241 TYR 0.021 0.001 TYR S 178 ARG 0.008 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 320) hydrogen bonds : angle 4.32156 ( 936) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.35140 ( 2) covalent geometry : bond 0.00331 ( 8636) covalent geometry : angle 0.59265 (11748) Misc. bond : bond 0.00141 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 253 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 316 THR cc_start: 0.8861 (m) cc_final: 0.8613 (p) REVERT: A 333 GLN cc_start: 0.8607 (tp40) cc_final: 0.8007 (tm-30) REVERT: B 217 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (pmm) REVERT: C 11 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6435 (tm-30) REVERT: C 21 MET cc_start: 0.8481 (tpp) cc_final: 0.8210 (mpp) REVERT: C 32 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7360 (tttp) REVERT: C 58 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: R 365 TYR cc_start: 0.7548 (t80) cc_final: 0.7219 (t80) REVERT: S 84 THR cc_start: 0.8301 (m) cc_final: 0.7961 (p) REVERT: S 189 ASP cc_start: 0.7822 (t0) cc_final: 0.7374 (m-30) REVERT: S 206 ARG cc_start: 0.8171 (ppt90) cc_final: 0.7254 (ptm160) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 1.0505 time to fit residues: 151.1580 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 LYS Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103847 restraints weight = 12022.926| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.02 r_work: 0.3249 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8638 Z= 0.158 Angle : 0.594 9.165 11750 Z= 0.311 Chirality : 0.042 0.210 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.064 57.980 1352 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.40 % Allowed : 21.97 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.34 (0.26), residues: 1101 helix: 1.08 (0.30), residues: 352 sheet: -0.22 (0.30), residues: 289 loop : -1.21 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.005 0.001 HIS R 143 PHE 0.021 0.002 PHE B 335 TYR 0.023 0.002 TYR S 178 ARG 0.008 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 320) hydrogen bonds : angle 4.43760 ( 936) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.36714 ( 2) covalent geometry : bond 0.00374 ( 8636) covalent geometry : angle 0.59405 (11748) Misc. bond : bond 0.00111 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.25 seconds wall clock time: 104 minutes 25.45 seconds (6265.45 seconds total)