Starting phenix.real_space_refine on Thu Jun 4 15:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xum_67271/06_2026/9xum_67271.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 P 4 5.49 5 S 50 5.16 5 C 8638 2.51 5 N 2322 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 422} Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 422} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3PG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3PG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3PG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3PG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.55, per 1000 atoms: 0.26 Number of scatterers: 13636 At special positions: 0 Unit cell: (109.976, 105.316, 114.636, 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 50 16.00 P 4 15.00 O 2622 8.00 N 2322 7.00 C 8638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS C 81 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 632.7 milliseconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 24 sheets defined 29.6% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.524A pdb=" N ARG A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.684A pdb=" N PHE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 322 through 333 removed outlier: 5.555A pdb=" N ILE A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.599A pdb=" N SER A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.693A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.521A pdb=" N GLY A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.537A pdb=" N THR B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.856A pdb=" N LYS B 184 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.746A pdb=" N PHE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.645A pdb=" N LYS B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.771A pdb=" N ASP B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.793A pdb=" N ALA B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.632A pdb=" N TYR C 104 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.740A pdb=" N TYR C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.657A pdb=" N PHE C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 4.353A pdb=" N LYS C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 322 through 333 removed outlier: 5.368A pdb=" N ILE C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Proline residue: C 329 - end of helix removed outlier: 3.761A pdb=" N SER C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 443 through 449 removed outlier: 3.774A pdb=" N LEU C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.591A pdb=" N THR D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 124 through 135 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 180 through 184 removed outlier: 4.009A pdb=" N LYS D 184 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 197 removed outlier: 3.735A pdb=" N PHE D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.840A pdb=" N SER D 206 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 207 " --> pdb=" O ALA D 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 207' Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.782A pdb=" N ASP D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 290 through 297 removed outlier: 3.834A pdb=" N LYS D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 330 through 336 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 445 through 456 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.488A pdb=" N ILE A 139 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU A 174 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 141 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 138 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 212 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY A 300 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 295 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 238 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 301 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 236 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.548A pdb=" N LEU A 252 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 265 " --> pdb=" O LEU A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.159A pdb=" N LYS A 391 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 407 " --> pdb=" O ILE A 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 424 current: chain 'B' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 414 through 416 current: chain 'B' and resid 431 through 437 removed outlier: 6.259A pdb=" N GLN B 431 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU B 470 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LYS B 433 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE B 472 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N THR B 435 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 467 " --> pdb=" O ILE B 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 484 through 485 current: chain 'B' and resid 501 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 500 through 502 removed outlier: 6.013A pdb=" N VAL A 417 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 401 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 409 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.223A pdb=" N LYS A 412 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 429 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 465 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 459 through 460 removed outlier: 5.514A pdb=" N GLY A 459 " --> pdb=" O ILE A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 174 removed outlier: 6.477A pdb=" N VAL B 139 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 173 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 141 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER B 92 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU B 142 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 94 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 93 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 216 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY B 304 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 301 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE B 246 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET B 303 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 244 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL B 305 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 239 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR B 344 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 241 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB2, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB3, first strand: chain 'B' and resid 461 through 462 removed outlier: 5.801A pdb=" N GLY B 461 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 478 " --> pdb=" O ILE B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.895A pdb=" N LYS C 138 " --> pdb=" O VAL C 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 170 through 173 current: chain 'C' and resid 261 through 265 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB7, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.043A pdb=" N LYS C 391 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 407 " --> pdb=" O ILE C 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 423 through 424 current: chain 'D' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 416 current: chain 'D' and resid 431 through 437 removed outlier: 6.262A pdb=" N GLN D 431 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU D 470 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LYS D 433 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE D 472 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR D 435 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS D 467 " --> pdb=" O ILE D 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 484 through 485 current: chain 'D' and resid 501 through 503 Processing sheet with id=AB8, first strand: chain 'C' and resid 499 through 502 removed outlier: 6.410A pdb=" N LEU C 434 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL C 417 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 401 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS D 393 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE D 409 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.178A pdb=" N LYS C 412 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N HIS C 465 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 459 through 460 removed outlier: 5.587A pdb=" N GLY C 459 " --> pdb=" O ILE C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 174 removed outlier: 6.484A pdb=" N VAL D 139 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU D 173 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 141 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 93 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER D 216 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY D 304 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA D 301 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 246 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N MET D 303 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE D 244 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL D 305 " --> pdb=" O SER D 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AC4, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AC5, first strand: chain 'D' and resid 256 through 257 Processing sheet with id=AC6, first strand: chain 'D' and resid 461 through 462 removed outlier: 5.725A pdb=" N GLY D 461 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG D 478 " --> pdb=" O ILE D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 338 hydrogen bonds defined for protein. 873 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: 2.07 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2329 1.31 - 1.44: 3553 1.44 - 1.56: 7928 1.56 - 1.69: 4 1.69 - 1.82: 82 Bond restraints: 13896 Sorted by residual: bond pdb=" C ARG D 110 " pdb=" O ARG D 110 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.22e-02 6.72e+03 1.66e+01 bond pdb=" C ARG B 110 " pdb=" O ARG B 110 " ideal model delta sigma weight residual 1.234 1.196 0.038 1.22e-02 6.72e+03 9.85e+00 bond pdb=" CA ARG B 110 " pdb=" CB ARG B 110 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.78e-02 3.16e+03 5.88e+00 bond pdb=" CA ARG B 110 " pdb=" C ARG B 110 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.24e-02 6.50e+03 3.30e+00 bond pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.20e-02 6.94e+03 3.25e+00 ... (remaining 13891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18579 2.19 - 4.38: 184 4.38 - 6.57: 41 6.57 - 8.77: 8 8.77 - 10.96: 2 Bond angle restraints: 18814 Sorted by residual: angle pdb=" C THR C 80 " pdb=" CA THR C 80 " pdb=" CB THR C 80 " ideal model delta sigma weight residual 112.06 105.48 6.58 1.57e+00 4.06e-01 1.76e+01 angle pdb=" NE ARG B 110 " pdb=" CZ ARG B 110 " pdb=" NH1 ARG B 110 " ideal model delta sigma weight residual 121.50 117.59 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" CB MET B 226 " pdb=" CG MET B 226 " pdb=" SD MET B 226 " ideal model delta sigma weight residual 112.70 123.66 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C THR C 80 " pdb=" N CYS C 81 " pdb=" CA CYS C 81 " ideal model delta sigma weight residual 121.50 116.84 4.66 1.43e+00 4.89e-01 1.06e+01 angle pdb=" CB MET C 276 " pdb=" CG MET C 276 " pdb=" SD MET C 276 " ideal model delta sigma weight residual 112.70 122.09 -9.39 3.00e+00 1.11e-01 9.79e+00 ... (remaining 18809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 7331 16.69 - 33.38: 742 33.38 - 50.06: 253 50.06 - 66.75: 54 66.75 - 83.44: 13 Dihedral angle restraints: 8393 sinusoidal: 3359 harmonic: 5034 Sorted by residual: dihedral pdb=" CA GLY C 498 " pdb=" C GLY C 498 " pdb=" N TYR C 499 " pdb=" CA TYR C 499 " ideal model delta harmonic sigma weight residual -180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLN B 230 " pdb=" C GLN B 230 " pdb=" N ASP B 231 " pdb=" CA ASP B 231 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLN D 230 " pdb=" C GLN D 230 " pdb=" N ASP D 231 " pdb=" CA ASP D 231 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 8390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1182 0.031 - 0.062: 540 0.062 - 0.094: 202 0.094 - 0.125: 163 0.125 - 0.156: 17 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE B 507 " pdb=" N ILE B 507 " pdb=" C ILE B 507 " pdb=" CB ILE B 507 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2101 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 388 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ASN B 388 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN B 388 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 389 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 243 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" CG ASP C 243 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP C 243 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP C 243 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 297 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 298 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.018 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5008 2.87 - 3.38: 12005 3.38 - 3.88: 22958 3.88 - 4.39: 27026 4.39 - 4.90: 46415 Nonbonded interactions: 113412 Sorted by model distance: nonbonded pdb=" NH1 ARG B 110 " pdb=" O4P 3PG B 601 " model vdw 2.360 3.120 nonbonded pdb=" NH1 ARG D 110 " pdb=" O4P 3PG D 601 " model vdw 2.401 3.120 nonbonded pdb=" O THR B 284 " pdb=" OG1 THR B 284 " model vdw 2.487 3.040 nonbonded pdb=" O SER A 147 " pdb=" OD1 ASN A 151 " model vdw 2.506 3.040 nonbonded pdb=" O ASN B 388 " pdb=" OD1 ASN B 388 " model vdw 2.517 3.040 ... (remaining 113407 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.070 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 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 : 0.005 0.050 13897 Z= 0.233 Angle : 0.615 10.956 18816 Z= 0.314 Chirality : 0.048 0.156 2104 Planarity : 0.004 0.042 2442 Dihedral : 15.698 83.441 5170 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.71 % Allowed : 23.08 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1736 helix: -0.03 (0.27), residues: 374 sheet: -1.15 (0.25), residues: 378 loop : -0.62 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 337 TYR 0.013 0.001 TYR B 376 PHE 0.016 0.001 PHE D 334 TRP 0.005 0.001 TRP B 199 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (13896) covalent geometry : angle 0.61506 / 0.31 (18814) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.43492 / 0.26 ( 2) hydrogen bonds : bond 0.19352 / 13.37 ( 338) hydrogen bonds : angle 7.88415 / 5.62 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.493 Fit side-chains REVERT: A 79 GLN cc_start: 0.4027 (OUTLIER) cc_final: 0.3799 (mt0) REVERT: A 145 PHE cc_start: 0.7705 (t80) cc_final: 0.7295 (t80) REVERT: A 156 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6848 (mmt-90) REVERT: A 178 GLN cc_start: 0.8132 (pt0) cc_final: 0.7634 (pt0) REVERT: A 220 ASP cc_start: 0.7975 (t0) cc_final: 0.7203 (t0) REVERT: A 254 LYS cc_start: 0.6682 (mttt) cc_final: 0.5480 (mmmt) REVERT: A 258 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7283 (pm20) REVERT: A 263 GLU cc_start: 0.7544 (tt0) cc_final: 0.6681 (tp30) REVERT: A 317 PHE cc_start: 0.7004 (m-80) cc_final: 0.6764 (m-80) REVERT: A 399 ASP cc_start: 0.7987 (t0) cc_final: 0.7518 (t70) REVERT: A 412 LYS cc_start: 0.7645 (tttp) cc_final: 0.6847 (tttm) REVERT: A 434 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 487 ASP cc_start: 0.7818 (m-30) cc_final: 0.7089 (t0) REVERT: A 494 ARG cc_start: 0.6003 (mmm-85) cc_final: 0.5653 (mmm160) REVERT: A 495 GLU cc_start: 0.7896 (tt0) cc_final: 0.7621 (tm-30) REVERT: B 102 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7432 (mtp180) REVERT: B 144 GLN cc_start: 0.8457 (pt0) cc_final: 0.7806 (tt0) REVERT: B 156 ARG cc_start: 0.7428 (mtp85) cc_final: 0.6869 (mtt-85) REVERT: B 185 ARG cc_start: 0.7242 (mtm180) cc_final: 0.5819 (mmp80) REVERT: B 300 ILE cc_start: 0.7494 (pt) cc_final: 0.7062 (pp) REVERT: B 311 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6620 (pm20) REVERT: B 320 ARG cc_start: 0.6755 (tpt90) cc_final: 0.5823 (tpp-160) REVERT: B 348 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 351 GLU cc_start: 0.7341 (tp30) cc_final: 0.6938 (tp30) REVERT: B 352 ASP cc_start: 0.7673 (t0) cc_final: 0.7377 (p0) REVERT: B 361 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6534 (mm-30) REVERT: B 395 ASP cc_start: 0.7512 (t0) cc_final: 0.7252 (t0) REVERT: B 396 ASN cc_start: 0.7657 (t0) cc_final: 0.7441 (t0) REVERT: B 398 LYS cc_start: 0.7807 (tttp) cc_final: 0.7486 (mtpp) REVERT: B 434 ASP cc_start: 0.8093 (m-30) cc_final: 0.7856 (m-30) REVERT: B 470 GLU cc_start: 0.7633 (tp30) cc_final: 0.7206 (tp30) REVERT: B 481 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6726 (ptmm) REVERT: B 517 LYS cc_start: 0.6916 (mttt) cc_final: 0.6343 (mtpm) REVERT: C 135 ASN cc_start: 0.8014 (m-40) cc_final: 0.7759 (m-40) REVERT: C 145 PHE cc_start: 0.7922 (t80) cc_final: 0.7625 (t80) REVERT: C 155 SER cc_start: 0.8056 (t) cc_final: 0.7771 (p) REVERT: C 156 ARG cc_start: 0.7210 (mtm180) cc_final: 0.6260 (mtt-85) REVERT: C 201 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7170 (mt-10) REVERT: C 252 LEU cc_start: 0.7398 (mm) cc_final: 0.7165 (mm) REVERT: C 293 MET cc_start: 0.5828 (mtt) cc_final: 0.5582 (mtt) REVERT: C 295 PHE cc_start: 0.6623 (m-80) cc_final: 0.6402 (m-80) REVERT: C 309 MET cc_start: 0.8134 (tpp) cc_final: 0.7844 (tpp) REVERT: C 316 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7707 (mp10) REVERT: C 354 GLU cc_start: 0.7250 (tt0) cc_final: 0.6744 (tp30) REVERT: C 365 LYS cc_start: 0.7096 (mtpt) cc_final: 0.6455 (mttt) REVERT: C 366 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6544 (mmtt) REVERT: C 431 GLU cc_start: 0.7902 (mt-10) cc_final: 0.6860 (tt0) REVERT: C 436 MET cc_start: 0.8665 (mmm) cc_final: 0.8203 (mtm) REVERT: C 494 ARG cc_start: 0.6154 (mmm-85) cc_final: 0.5917 (mtt90) REVERT: D 102 ARG cc_start: 0.7165 (mtp180) cc_final: 0.6940 (mtm180) REVERT: D 109 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (ptp-110) REVERT: D 144 GLN cc_start: 0.8333 (tt0) cc_final: 0.7792 (tt0) REVERT: D 156 ARG cc_start: 0.7026 (mtp85) cc_final: 0.5899 (mmt-90) REVERT: D 184 LYS cc_start: 0.6060 (mttp) cc_final: 0.5630 (ttmt) REVERT: D 185 ARG cc_start: 0.6879 (mtm180) cc_final: 0.5884 (mmm160) REVERT: D 192 ASP cc_start: 0.7415 (t0) cc_final: 0.7077 (t0) REVERT: D 208 ASP cc_start: 0.7430 (m-30) cc_final: 0.6711 (p0) REVERT: D 227 ASP cc_start: 0.7746 (m-30) cc_final: 0.7421 (m-30) REVERT: D 256 LEU cc_start: 0.7922 (mp) cc_final: 0.7647 (mm) REVERT: D 311 GLU cc_start: 0.6947 (pt0) cc_final: 0.6535 (pm20) REVERT: D 320 ARG cc_start: 0.6850 (mmm160) cc_final: 0.6636 (mmm160) REVERT: D 348 ASP cc_start: 0.7607 (t0) cc_final: 0.6969 (m-30) REVERT: D 351 GLU cc_start: 0.7132 (tp30) cc_final: 0.6792 (mm-30) REVERT: D 361 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6971 (mm-30) REVERT: D 424 SER cc_start: 0.8542 (t) cc_final: 0.8265 (p) REVERT: D 464 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 481 LYS cc_start: 0.7313 (ptpt) cc_final: 0.6987 (ptmt) REVERT: D 489 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6792 (tt0) REVERT: D 496 ARG cc_start: 0.6387 (mmm-85) cc_final: 0.6115 (mmm160) outliers start: 25 outliers final: 9 residues processed: 253 average time/residue: 0.6764 time to fit residues: 184.7892 Evaluate side-chains 228 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 411 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 161 ASN B 315 ASN C 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106428 restraints weight = 15144.683| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.07 r_work: 0.3049 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13897 Z= 0.145 Angle : 0.512 6.651 18816 Z= 0.271 Chirality : 0.048 0.138 2104 Planarity : 0.004 0.034 2442 Dihedral : 6.096 61.037 1982 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.49 % Allowed : 20.55 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1736 helix: 0.09 (0.26), residues: 400 sheet: -1.05 (0.25), residues: 382 loop : -0.61 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.014 0.001 TYR C 357 PHE 0.017 0.001 PHE D 360 TRP 0.004 0.001 TRP A 185 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (13896) covalent geometry : angle 0.51145 / 0.27 (18814) SS BOND : bond 0.00153 / 0.08 ( 1) SS BOND : angle 1.04314 / 0.61 ( 2) hydrogen bonds : bond 0.03944 / 2.66 ( 338) hydrogen bonds : angle 5.78970 / 4.19 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 144 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: A 145 PHE cc_start: 0.8391 (t80) cc_final: 0.8125 (t80) REVERT: A 156 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7762 (mmt-90) REVERT: A 220 ASP cc_start: 0.8431 (t0) cc_final: 0.7912 (t0) REVERT: A 254 LYS cc_start: 0.7562 (mttt) cc_final: 0.6295 (mmmt) REVERT: A 260 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6824 (ttt180) REVERT: A 263 GLU cc_start: 0.7654 (tt0) cc_final: 0.7157 (tp30) REVERT: A 336 LEU cc_start: 0.7928 (mp) cc_final: 0.7728 (mt) REVERT: A 337 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7320 (ttm170) REVERT: A 348 GLU cc_start: 0.8059 (tp30) cc_final: 0.7799 (tp30) REVERT: A 399 ASP cc_start: 0.8657 (t0) cc_final: 0.8263 (t70) REVERT: A 412 LYS cc_start: 0.8585 (tttp) cc_final: 0.8225 (tttm) REVERT: A 487 ASP cc_start: 0.7965 (m-30) cc_final: 0.7356 (t0) REVERT: A 491 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 494 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6971 (mmm160) REVERT: A 495 GLU cc_start: 0.8168 (tt0) cc_final: 0.7899 (tm-30) REVERT: B 102 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7932 (mtp180) REVERT: B 144 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: B 156 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7859 (mtt-85) REVERT: B 351 GLU cc_start: 0.7945 (tp30) cc_final: 0.7685 (tp30) REVERT: B 352 ASP cc_start: 0.7848 (t0) cc_final: 0.7563 (p0) REVERT: B 361 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7687 (mm-30) REVERT: B 395 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t0) REVERT: B 396 ASN cc_start: 0.8519 (t0) cc_final: 0.8273 (t0) REVERT: B 398 LYS cc_start: 0.8600 (tttp) cc_final: 0.8357 (mtpp) REVERT: B 470 GLU cc_start: 0.7997 (tp30) cc_final: 0.7620 (tp30) REVERT: B 481 LYS cc_start: 0.8466 (pttt) cc_final: 0.7843 (ptmm) REVERT: B 517 LYS cc_start: 0.7553 (mttt) cc_final: 0.7077 (mtpm) REVERT: C 155 SER cc_start: 0.8773 (t) cc_final: 0.8471 (m) REVERT: C 156 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7369 (mtt-85) REVERT: C 177 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 295 PHE cc_start: 0.7383 (m-80) cc_final: 0.7151 (m-80) REVERT: C 309 MET cc_start: 0.8810 (tpp) cc_final: 0.8495 (tpp) REVERT: C 316 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8185 (mp10) REVERT: C 354 GLU cc_start: 0.8061 (tt0) cc_final: 0.7705 (tp30) REVERT: C 365 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7217 (mttt) REVERT: C 431 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7940 (tt0) REVERT: C 436 MET cc_start: 0.9175 (mmm) cc_final: 0.8664 (mtm) REVERT: D 102 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7652 (mtm180) REVERT: D 144 GLN cc_start: 0.8902 (tt0) cc_final: 0.8688 (tt0) REVERT: D 156 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7115 (mmt-90) REVERT: D 184 LYS cc_start: 0.6793 (mttp) cc_final: 0.6511 (ttmt) REVERT: D 185 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6448 (mmm160) REVERT: D 192 ASP cc_start: 0.8391 (t0) cc_final: 0.8122 (t0) REVERT: D 208 ASP cc_start: 0.7585 (m-30) cc_final: 0.7125 (p0) REVERT: D 227 ASP cc_start: 0.8439 (m-30) cc_final: 0.8159 (m-30) REVERT: D 293 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5511 (tt0) REVERT: D 296 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6191 (mppt) REVERT: D 311 GLU cc_start: 0.7673 (pt0) cc_final: 0.7429 (pm20) REVERT: D 320 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7301 (mmm160) REVERT: D 348 ASP cc_start: 0.8019 (t0) cc_final: 0.7639 (m-30) REVERT: D 351 GLU cc_start: 0.7831 (tp30) cc_final: 0.7484 (mm-30) REVERT: D 361 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7899 (mm-30) REVERT: D 455 GLU cc_start: 0.7001 (tt0) cc_final: 0.6719 (mt-10) REVERT: D 464 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 481 LYS cc_start: 0.8414 (ptpt) cc_final: 0.8093 (ptmt) REVERT: D 496 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.7229 (mmm160) outliers start: 51 outliers final: 14 residues processed: 256 average time/residue: 0.6559 time to fit residues: 181.9734 Evaluate side-chains 214 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 66 optimal weight: 0.0970 chunk 165 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101006 restraints weight = 15306.256| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.99 r_work: 0.2974 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13897 Z= 0.175 Angle : 0.521 6.848 18816 Z= 0.277 Chirality : 0.048 0.138 2104 Planarity : 0.004 0.032 2442 Dihedral : 5.167 55.684 1954 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.42 % Allowed : 20.55 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1736 helix: 0.15 (0.26), residues: 400 sheet: -1.04 (0.24), residues: 396 loop : -0.71 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 318 TYR 0.014 0.001 TYR C 357 PHE 0.016 0.002 PHE D 360 TRP 0.004 0.001 TRP D 186 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13896) covalent geometry : angle 0.52149 / 0.28 (18814) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 0.52117 / 0.31 ( 2) hydrogen bonds : bond 0.03681 / 2.45 ( 338) hydrogen bonds : angle 5.45630 / 3.93 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.500 Fit side-chains REVERT: A 144 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8952 (tt0) REVERT: A 145 PHE cc_start: 0.8532 (t80) cc_final: 0.8234 (t80) REVERT: A 156 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7914 (mmt-90) REVERT: A 220 ASP cc_start: 0.8462 (t0) cc_final: 0.8008 (t0) REVERT: A 254 LYS cc_start: 0.7727 (mttt) cc_final: 0.6503 (mmmt) REVERT: A 258 GLU cc_start: 0.7576 (pm20) cc_final: 0.7304 (pt0) REVERT: A 263 GLU cc_start: 0.7663 (tt0) cc_final: 0.7290 (tp30) REVERT: A 348 GLU cc_start: 0.8154 (tp30) cc_final: 0.7885 (tp30) REVERT: A 399 ASP cc_start: 0.8685 (t0) cc_final: 0.8325 (t70) REVERT: A 412 LYS cc_start: 0.8662 (tttp) cc_final: 0.8324 (tttm) REVERT: A 487 ASP cc_start: 0.7928 (m-30) cc_final: 0.7420 (t0) REVERT: A 491 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 494 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7020 (mmm160) REVERT: A 495 GLU cc_start: 0.8226 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 102 ARG cc_start: 0.8277 (mtm180) cc_final: 0.8006 (mtp180) REVERT: B 144 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: B 184 LYS cc_start: 0.7368 (mttm) cc_final: 0.6818 (mtpt) REVERT: B 320 ARG cc_start: 0.7714 (mmm160) cc_final: 0.6450 (tpp-160) REVERT: B 352 ASP cc_start: 0.7792 (t0) cc_final: 0.7425 (p0) REVERT: B 361 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7838 (mm-30) REVERT: B 396 ASN cc_start: 0.8569 (t0) cc_final: 0.8367 (t0) REVERT: B 470 GLU cc_start: 0.8079 (tp30) cc_final: 0.7860 (tp30) REVERT: B 481 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8048 (ptmt) REVERT: B 517 LYS cc_start: 0.7675 (mttt) cc_final: 0.7229 (mtpm) REVERT: C 155 SER cc_start: 0.8819 (t) cc_final: 0.8499 (m) REVERT: C 156 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7548 (mtt-85) REVERT: C 177 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: C 309 MET cc_start: 0.8829 (tpp) cc_final: 0.8525 (tpp) REVERT: C 316 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8106 (mp10) REVERT: C 354 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: C 365 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7398 (mttt) REVERT: C 431 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8101 (tt0) REVERT: C 436 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8676 (mtm) REVERT: C 494 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.7012 (mmt90) REVERT: D 102 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7816 (mtm180) REVERT: D 156 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7382 (mmt-90) REVERT: D 184 LYS cc_start: 0.6977 (mttp) cc_final: 0.6733 (ttmt) REVERT: D 185 ARG cc_start: 0.7333 (mtm180) cc_final: 0.7039 (mtp180) REVERT: D 192 ASP cc_start: 0.8480 (t0) cc_final: 0.8230 (t0) REVERT: D 208 ASP cc_start: 0.7612 (m-30) cc_final: 0.7187 (p0) REVERT: D 227 ASP cc_start: 0.8575 (m-30) cc_final: 0.8332 (m-30) REVERT: D 256 LEU cc_start: 0.8058 (mp) cc_final: 0.7802 (mm) REVERT: D 293 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5533 (tt0) REVERT: D 296 LYS cc_start: 0.6999 (mtpp) cc_final: 0.6107 (mppt) REVERT: D 311 GLU cc_start: 0.7805 (pt0) cc_final: 0.7579 (pm20) REVERT: D 320 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7435 (mmm160) REVERT: D 326 ASP cc_start: 0.7554 (m-30) cc_final: 0.7126 (m-30) REVERT: D 348 ASP cc_start: 0.8058 (t0) cc_final: 0.7735 (m-30) REVERT: D 351 GLU cc_start: 0.7990 (tp30) cc_final: 0.7671 (mm-30) REVERT: D 455 GLU cc_start: 0.7132 (tt0) cc_final: 0.6879 (mt-10) REVERT: D 464 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 481 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8266 (ptmt) REVERT: D 493 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7850 (mm-30) outliers start: 50 outliers final: 26 residues processed: 231 average time/residue: 0.6489 time to fit residues: 162.8486 Evaluate side-chains 218 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 142 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107853 restraints weight = 15216.606| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.07 r_work: 0.3052 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13897 Z= 0.103 Angle : 0.468 6.722 18816 Z= 0.248 Chirality : 0.047 0.170 2104 Planarity : 0.003 0.035 2442 Dihedral : 4.937 55.691 1954 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.42 % Allowed : 20.68 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1736 helix: 0.35 (0.26), residues: 400 sheet: -1.01 (0.24), residues: 396 loop : -0.65 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 337 TYR 0.015 0.001 TYR C 357 PHE 0.014 0.001 PHE D 360 TRP 0.005 0.001 TRP D 186 HIS 0.003 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (13896) covalent geometry : angle 0.46850 / 0.25 (18814) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.41159 / 0.24 ( 2) hydrogen bonds : bond 0.03102 / 2.07 ( 338) hydrogen bonds : angle 5.12994 / 3.69 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.554 Fit side-chains REVERT: A 103 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 144 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8732 (tt0) REVERT: A 145 PHE cc_start: 0.8368 (t80) cc_final: 0.8061 (t80) REVERT: A 156 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7605 (mmt-90) REVERT: A 220 ASP cc_start: 0.8394 (t0) cc_final: 0.7843 (t0) REVERT: A 254 LYS cc_start: 0.7467 (mttt) cc_final: 0.6238 (mmmt) REVERT: A 263 GLU cc_start: 0.7585 (tt0) cc_final: 0.7054 (tp30) REVERT: A 276 MET cc_start: 0.6222 (mtt) cc_final: 0.5876 (mtt) REVERT: A 348 GLU cc_start: 0.8028 (tp30) cc_final: 0.7784 (tp30) REVERT: A 399 ASP cc_start: 0.8581 (t0) cc_final: 0.8248 (t70) REVERT: A 412 LYS cc_start: 0.8485 (tttp) cc_final: 0.8093 (tttm) REVERT: A 487 ASP cc_start: 0.7940 (m-30) cc_final: 0.7352 (t0) REVERT: A 491 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 494 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6539 (mmm160) REVERT: A 495 GLU cc_start: 0.8107 (tt0) cc_final: 0.7865 (tm-30) REVERT: B 102 ARG cc_start: 0.8095 (mtm180) cc_final: 0.7842 (mtp180) REVERT: B 144 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: B 184 LYS cc_start: 0.7120 (mttm) cc_final: 0.6636 (mtpt) REVERT: B 320 ARG cc_start: 0.7579 (mmm160) cc_final: 0.6255 (tpp-160) REVERT: B 348 ASP cc_start: 0.8440 (t0) cc_final: 0.8100 (m-30) REVERT: B 352 ASP cc_start: 0.7786 (t0) cc_final: 0.7394 (p0) REVERT: B 361 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7458 (mm-30) REVERT: B 396 ASN cc_start: 0.8441 (t0) cc_final: 0.8208 (t0) REVERT: B 398 LYS cc_start: 0.8539 (tttp) cc_final: 0.8289 (mtpp) REVERT: B 470 GLU cc_start: 0.7910 (tp30) cc_final: 0.7571 (tp30) REVERT: B 481 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7712 (ptmm) REVERT: B 517 LYS cc_start: 0.7482 (mttt) cc_final: 0.6984 (mtpm) REVERT: C 155 SER cc_start: 0.8671 (t) cc_final: 0.8404 (m) REVERT: C 156 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7144 (mtt-85) REVERT: C 309 MET cc_start: 0.8716 (tpp) cc_final: 0.8391 (tpp) REVERT: C 354 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: C 365 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7260 (mttt) REVERT: C 431 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7812 (tt0) REVERT: C 494 ARG cc_start: 0.6978 (mmm-85) cc_final: 0.6757 (mmt90) REVERT: D 102 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7594 (mtm180) REVERT: D 156 ARG cc_start: 0.7732 (mtp85) cc_final: 0.6967 (mmt-90) REVERT: D 184 LYS cc_start: 0.6817 (mttp) cc_final: 0.6544 (ttmt) REVERT: D 185 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6495 (mmm160) REVERT: D 192 ASP cc_start: 0.8306 (t0) cc_final: 0.7991 (t0) REVERT: D 208 ASP cc_start: 0.7556 (m-30) cc_final: 0.7040 (p0) REVERT: D 244 ILE cc_start: 0.8306 (tp) cc_final: 0.7953 (pt) REVERT: D 293 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5490 (tt0) REVERT: D 296 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6187 (mppt) REVERT: D 311 GLU cc_start: 0.7577 (pt0) cc_final: 0.7301 (pm20) REVERT: D 312 ILE cc_start: 0.8573 (mm) cc_final: 0.8367 (mp) REVERT: D 326 ASP cc_start: 0.7419 (m-30) cc_final: 0.6991 (m-30) REVERT: D 348 ASP cc_start: 0.7971 (t0) cc_final: 0.7566 (m-30) REVERT: D 351 GLU cc_start: 0.7987 (tp30) cc_final: 0.7642 (mm-30) REVERT: D 455 GLU cc_start: 0.6931 (tt0) cc_final: 0.6596 (mt-10) REVERT: D 464 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: D 481 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7934 (ptmt) REVERT: D 493 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7757 (mm-30) outliers start: 50 outliers final: 19 residues processed: 234 average time/residue: 0.6772 time to fit residues: 171.8563 Evaluate side-chains 222 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 171 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 159 optimal weight: 0.0980 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 196 GLN B 315 ASN C 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109662 restraints weight = 15274.252| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.06 r_work: 0.3093 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13897 Z= 0.090 Angle : 0.458 6.926 18816 Z= 0.241 Chirality : 0.046 0.135 2104 Planarity : 0.003 0.038 2442 Dihedral : 4.792 56.639 1954 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.08 % Allowed : 21.64 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1736 helix: 0.52 (0.26), residues: 398 sheet: -0.87 (0.25), residues: 392 loop : -0.61 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 337 TYR 0.017 0.001 TYR B 299 PHE 0.013 0.001 PHE D 360 TRP 0.005 0.001 TRP D 186 HIS 0.002 0.000 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (13896) covalent geometry : angle 0.45780 / 0.24 (18814) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.30959 / 0.18 ( 2) hydrogen bonds : bond 0.02930 / 1.96 ( 338) hydrogen bonds : angle 4.92564 / 3.54 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.495 Fit side-chains REVERT: A 144 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: A 145 PHE cc_start: 0.8432 (t80) cc_final: 0.8130 (t80) REVERT: A 156 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7659 (mmt-90) REVERT: A 172 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: A 214 ASP cc_start: 0.8359 (p0) cc_final: 0.8073 (p0) REVERT: A 220 ASP cc_start: 0.8457 (t0) cc_final: 0.7933 (t0) REVERT: A 254 LYS cc_start: 0.7530 (mttt) cc_final: 0.6277 (mmmt) REVERT: A 263 GLU cc_start: 0.7566 (tt0) cc_final: 0.7099 (tp30) REVERT: A 276 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5814 (mtp) REVERT: A 348 GLU cc_start: 0.8077 (tp30) cc_final: 0.7789 (tp30) REVERT: A 399 ASP cc_start: 0.8563 (t0) cc_final: 0.8258 (t70) REVERT: A 412 LYS cc_start: 0.8562 (tttp) cc_final: 0.7770 (tptt) REVERT: A 494 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6635 (mmm160) REVERT: B 102 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7906 (mtp180) REVERT: B 144 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: B 184 LYS cc_start: 0.7068 (mttm) cc_final: 0.6616 (mtpt) REVERT: B 280 MET cc_start: 0.6101 (mmm) cc_final: 0.5483 (mmt) REVERT: B 320 ARG cc_start: 0.7623 (mmm160) cc_final: 0.6319 (tpp-160) REVERT: B 348 ASP cc_start: 0.8387 (t0) cc_final: 0.8127 (m-30) REVERT: B 352 ASP cc_start: 0.7735 (t0) cc_final: 0.7365 (p0) REVERT: B 361 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7542 (mm-30) REVERT: B 470 GLU cc_start: 0.7917 (tp30) cc_final: 0.7661 (tp30) REVERT: B 481 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7779 (ptmm) REVERT: B 517 LYS cc_start: 0.7544 (mttt) cc_final: 0.7047 (mtpm) REVERT: C 156 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7171 (mtt-85) REVERT: C 309 MET cc_start: 0.8764 (tpp) cc_final: 0.8436 (tpp) REVERT: C 354 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: C 365 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7269 (mttt) REVERT: C 431 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7900 (tt0) REVERT: C 494 ARG cc_start: 0.7090 (mmm-85) cc_final: 0.6873 (mmt90) REVERT: D 102 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7684 (mtm180) REVERT: D 156 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7229 (mmm160) REVERT: D 184 LYS cc_start: 0.6827 (mttp) cc_final: 0.6534 (ttmt) REVERT: D 185 ARG cc_start: 0.7270 (mtm180) cc_final: 0.6558 (mmm160) REVERT: D 192 ASP cc_start: 0.8350 (t0) cc_final: 0.8077 (t0) REVERT: D 208 ASP cc_start: 0.7516 (m-30) cc_final: 0.7078 (p0) REVERT: D 227 ASP cc_start: 0.8475 (m-30) cc_final: 0.8204 (m-30) REVERT: D 244 ILE cc_start: 0.8402 (tp) cc_final: 0.8119 (pt) REVERT: D 256 LEU cc_start: 0.7767 (mp) cc_final: 0.7483 (mm) REVERT: D 293 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5534 (tt0) REVERT: D 296 LYS cc_start: 0.7017 (mtpp) cc_final: 0.6163 (mppt) REVERT: D 311 GLU cc_start: 0.7647 (pt0) cc_final: 0.7416 (pm20) REVERT: D 326 ASP cc_start: 0.7383 (m-30) cc_final: 0.7029 (m-30) REVERT: D 348 ASP cc_start: 0.8048 (t0) cc_final: 0.7641 (m-30) REVERT: D 351 GLU cc_start: 0.7970 (tp30) cc_final: 0.7673 (mm-30) REVERT: D 455 GLU cc_start: 0.7009 (tt0) cc_final: 0.6692 (mt-10) REVERT: D 464 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: D 481 LYS cc_start: 0.8332 (ptpt) cc_final: 0.8013 (ptmt) REVERT: D 493 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7855 (mm-30) outliers start: 45 outliers final: 20 residues processed: 237 average time/residue: 0.6534 time to fit residues: 168.3352 Evaluate side-chains 226 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 137 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 159 optimal weight: 0.0370 chunk 109 optimal weight: 5.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 457 ASN C 144 GLN D 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100302 restraints weight = 15416.387| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.99 r_work: 0.2967 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13897 Z= 0.236 Angle : 0.569 8.638 18816 Z= 0.299 Chirality : 0.050 0.143 2104 Planarity : 0.004 0.035 2442 Dihedral : 5.283 56.190 1954 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.49 % Allowed : 21.71 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1736 helix: 0.16 (0.26), residues: 402 sheet: -1.01 (0.24), residues: 406 loop : -0.70 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 337 TYR 0.014 0.002 TYR C 357 PHE 0.016 0.002 PHE D 409 TRP 0.004 0.001 TRP D 186 HIS 0.007 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (13896) covalent geometry : angle 0.56856 / 0.30 (18814) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.46616 / 0.27 ( 2) hydrogen bonds : bond 0.03699 / 2.44 ( 338) hydrogen bonds : angle 5.23569 / 3.76 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.538 Fit side-chains REVERT: A 145 PHE cc_start: 0.8562 (t80) cc_final: 0.8276 (t80) REVERT: A 220 ASP cc_start: 0.8463 (t0) cc_final: 0.8029 (t0) REVERT: A 254 LYS cc_start: 0.7709 (mttt) cc_final: 0.6530 (mmmt) REVERT: A 263 GLU cc_start: 0.7682 (tt0) cc_final: 0.7226 (tp30) REVERT: A 276 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.6163 (mtt) REVERT: A 348 GLU cc_start: 0.8258 (tp30) cc_final: 0.8007 (tp30) REVERT: A 399 ASP cc_start: 0.8727 (t0) cc_final: 0.8446 (t70) REVERT: A 412 LYS cc_start: 0.8702 (tttp) cc_final: 0.8094 (tptt) REVERT: A 487 ASP cc_start: 0.8000 (m-30) cc_final: 0.7491 (t0) REVERT: A 491 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: A 494 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.7202 (mmm160) REVERT: B 102 ARG cc_start: 0.8328 (mtm180) cc_final: 0.8056 (mtp180) REVERT: B 144 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: B 184 LYS cc_start: 0.7463 (mttm) cc_final: 0.6907 (mtpt) REVERT: B 320 ARG cc_start: 0.7654 (mmm160) cc_final: 0.6377 (tpp-160) REVERT: B 352 ASP cc_start: 0.7714 (t0) cc_final: 0.7369 (p0) REVERT: B 361 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7809 (mm-30) REVERT: B 481 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8074 (ptmt) REVERT: B 517 LYS cc_start: 0.7677 (mttt) cc_final: 0.7236 (mtpm) REVERT: C 156 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7441 (mtt-85) REVERT: C 293 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.5666 (mtp) REVERT: C 309 MET cc_start: 0.8848 (tpp) cc_final: 0.8514 (tpp) REVERT: C 354 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: C 365 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7417 (mttt) REVERT: C 431 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8126 (tt0) REVERT: C 494 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6793 (mmm-85) REVERT: D 102 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7870 (mtm180) REVERT: D 156 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7467 (mmt-90) REVERT: D 184 LYS cc_start: 0.7117 (mttp) cc_final: 0.6787 (ttmt) REVERT: D 185 ARG cc_start: 0.7409 (mtm180) cc_final: 0.6637 (mmm160) REVERT: D 192 ASP cc_start: 0.8584 (t0) cc_final: 0.8280 (t0) REVERT: D 208 ASP cc_start: 0.7641 (m-30) cc_final: 0.7146 (p0) REVERT: D 256 LEU cc_start: 0.8193 (mp) cc_final: 0.7929 (mm) REVERT: D 293 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5538 (tt0) REVERT: D 311 GLU cc_start: 0.7824 (pt0) cc_final: 0.7582 (pm20) REVERT: D 326 ASP cc_start: 0.7465 (m-30) cc_final: 0.7138 (m-30) REVERT: D 348 ASP cc_start: 0.8024 (t0) cc_final: 0.7729 (m-30) REVERT: D 351 GLU cc_start: 0.8102 (tp30) cc_final: 0.7803 (mm-30) REVERT: D 455 GLU cc_start: 0.7095 (tt0) cc_final: 0.6869 (mt-10) REVERT: D 464 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: D 481 LYS cc_start: 0.8592 (ptpt) cc_final: 0.8293 (ptmt) REVERT: D 493 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7920 (mm-30) outliers start: 51 outliers final: 24 residues processed: 221 average time/residue: 0.7116 time to fit residues: 170.0662 Evaluate side-chains 209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 109 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107303 restraints weight = 15230.380| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.06 r_work: 0.3053 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13897 Z= 0.113 Angle : 0.492 8.986 18816 Z= 0.258 Chirality : 0.047 0.135 2104 Planarity : 0.003 0.038 2442 Dihedral : 5.030 57.551 1954 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.81 % Allowed : 22.26 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1736 helix: 0.37 (0.26), residues: 398 sheet: -0.96 (0.24), residues: 398 loop : -0.64 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.015 0.001 TYR C 357 PHE 0.014 0.001 PHE D 360 TRP 0.005 0.001 TRP D 186 HIS 0.004 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (13896) covalent geometry : angle 0.49170 / 0.26 (18814) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.34223 / 0.20 ( 2) hydrogen bonds : bond 0.03053 / 2.03 ( 338) hydrogen bonds : angle 5.02720 / 3.61 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.588 Fit side-chains REVERT: A 144 GLN cc_start: 0.8989 (pt0) cc_final: 0.8636 (tt0) REVERT: A 145 PHE cc_start: 0.8408 (t80) cc_final: 0.8074 (t80) REVERT: A 187 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7926 (mm-40) REVERT: A 220 ASP cc_start: 0.8396 (t0) cc_final: 0.7854 (t0) REVERT: A 254 LYS cc_start: 0.7577 (mttt) cc_final: 0.6308 (mmmt) REVERT: A 258 GLU cc_start: 0.7911 (pm20) cc_final: 0.7404 (pt0) REVERT: A 263 GLU cc_start: 0.7584 (tt0) cc_final: 0.7074 (tp30) REVERT: A 276 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6057 (mtt) REVERT: A 348 GLU cc_start: 0.8156 (tp30) cc_final: 0.7882 (tp30) REVERT: A 399 ASP cc_start: 0.8633 (t0) cc_final: 0.8396 (t70) REVERT: A 412 LYS cc_start: 0.8588 (tttp) cc_final: 0.7824 (tptt) REVERT: A 487 ASP cc_start: 0.8019 (m-30) cc_final: 0.7436 (t0) REVERT: A 488 ASN cc_start: 0.8122 (t0) cc_final: 0.7651 (t0) REVERT: A 490 GLN cc_start: 0.8132 (tp40) cc_final: 0.7855 (mm110) REVERT: A 494 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6827 (mmm160) REVERT: B 102 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7924 (mtp180) REVERT: B 144 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 184 LYS cc_start: 0.7163 (mttm) cc_final: 0.6677 (mtpt) REVERT: B 226 MET cc_start: 0.8907 (mmm) cc_final: 0.8592 (mmp) REVERT: B 270 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: B 320 ARG cc_start: 0.7528 (mmm160) cc_final: 0.6202 (tpp-160) REVERT: B 348 ASP cc_start: 0.8433 (t0) cc_final: 0.8112 (m-30) REVERT: B 352 ASP cc_start: 0.7737 (t0) cc_final: 0.7345 (p0) REVERT: B 361 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7536 (mm-30) REVERT: B 433 LYS cc_start: 0.8174 (tttt) cc_final: 0.7670 (ttpt) REVERT: B 470 GLU cc_start: 0.8273 (tp30) cc_final: 0.8067 (tp30) REVERT: B 481 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7738 (ptmm) REVERT: B 517 LYS cc_start: 0.7603 (mttt) cc_final: 0.7078 (mtpm) REVERT: C 156 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7151 (mtt-85) REVERT: C 309 MET cc_start: 0.8768 (tpp) cc_final: 0.8453 (tpp) REVERT: C 354 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: C 365 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7266 (mttt) REVERT: C 431 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7844 (tt0) REVERT: C 494 ARG cc_start: 0.7008 (mmm-85) cc_final: 0.6572 (mmm-85) REVERT: D 102 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7715 (mtm180) REVERT: D 156 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7072 (mmt-90) REVERT: D 184 LYS cc_start: 0.7008 (mttp) cc_final: 0.6758 (ttmt) REVERT: D 185 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6948 (mtp180) REVERT: D 192 ASP cc_start: 0.8336 (t0) cc_final: 0.8103 (t0) REVERT: D 208 ASP cc_start: 0.7566 (m-30) cc_final: 0.6992 (p0) REVERT: D 256 LEU cc_start: 0.7888 (mp) cc_final: 0.7570 (mm) REVERT: D 293 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5474 (tt0) REVERT: D 311 GLU cc_start: 0.7643 (pt0) cc_final: 0.7404 (pm20) REVERT: D 326 ASP cc_start: 0.7340 (m-30) cc_final: 0.7007 (m-30) REVERT: D 348 ASP cc_start: 0.8026 (t0) cc_final: 0.7609 (m-30) REVERT: D 351 GLU cc_start: 0.7950 (tp30) cc_final: 0.7631 (mm-30) REVERT: D 455 GLU cc_start: 0.7048 (tt0) cc_final: 0.6704 (mt-10) REVERT: D 464 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: D 481 LYS cc_start: 0.8320 (ptpt) cc_final: 0.7996 (ptmt) REVERT: D 493 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7876 (mm-30) outliers start: 41 outliers final: 22 residues processed: 220 average time/residue: 0.6787 time to fit residues: 161.7024 Evaluate side-chains 212 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 166 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102223 restraints weight = 15292.910| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.97 r_work: 0.2998 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13897 Z= 0.144 Angle : 0.513 9.497 18816 Z= 0.268 Chirality : 0.047 0.180 2104 Planarity : 0.004 0.039 2442 Dihedral : 5.086 57.951 1954 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.60 % Allowed : 22.53 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1736 helix: 0.32 (0.26), residues: 402 sheet: -0.95 (0.24), residues: 398 loop : -0.64 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.015 0.001 TYR C 357 PHE 0.014 0.001 PHE D 360 TRP 0.004 0.001 TRP D 186 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (13896) covalent geometry : angle 0.51260 / 0.27 (18814) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.35867 / 0.21 ( 2) hydrogen bonds : bond 0.03214 / 2.14 ( 338) hydrogen bonds : angle 5.02169 / 3.60 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.447 Fit side-chains REVERT: A 145 PHE cc_start: 0.8516 (t80) cc_final: 0.8224 (t80) REVERT: A 220 ASP cc_start: 0.8420 (t0) cc_final: 0.7974 (t0) REVERT: A 254 LYS cc_start: 0.7721 (mttt) cc_final: 0.6530 (mmmt) REVERT: A 258 GLU cc_start: 0.7725 (pm20) cc_final: 0.7278 (pt0) REVERT: A 263 GLU cc_start: 0.7631 (tt0) cc_final: 0.7196 (tp30) REVERT: A 276 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6174 (mtt) REVERT: A 348 GLU cc_start: 0.8301 (tp30) cc_final: 0.8038 (tp30) REVERT: A 383 GLN cc_start: 0.7907 (tt0) cc_final: 0.7558 (tp-100) REVERT: A 399 ASP cc_start: 0.8679 (t0) cc_final: 0.8424 (t70) REVERT: A 412 LYS cc_start: 0.8698 (tttp) cc_final: 0.8029 (tptt) REVERT: A 487 ASP cc_start: 0.7992 (m-30) cc_final: 0.7495 (t0) REVERT: A 488 ASN cc_start: 0.8220 (t0) cc_final: 0.7782 (t0) REVERT: A 494 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.7091 (mmm160) REVERT: B 102 ARG cc_start: 0.8330 (mtm180) cc_final: 0.8048 (mtp180) REVERT: B 144 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: B 184 LYS cc_start: 0.7383 (mttm) cc_final: 0.6862 (mtpt) REVERT: B 320 ARG cc_start: 0.7649 (mmm160) cc_final: 0.6429 (tpp-160) REVERT: B 348 ASP cc_start: 0.8471 (t0) cc_final: 0.8222 (m-30) REVERT: B 352 ASP cc_start: 0.7703 (t0) cc_final: 0.7365 (p0) REVERT: B 481 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8156 (ptmt) REVERT: B 517 LYS cc_start: 0.7661 (mttt) cc_final: 0.7209 (mtpm) REVERT: C 156 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7424 (mtt-85) REVERT: C 293 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5566 (mtp) REVERT: C 309 MET cc_start: 0.8832 (tpp) cc_final: 0.8526 (tpp) REVERT: C 354 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: C 365 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7446 (mttt) REVERT: C 431 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8060 (tt0) REVERT: C 494 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6790 (mmm-85) REVERT: D 102 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7871 (mtm180) REVERT: D 156 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7437 (mmt-90) REVERT: D 184 LYS cc_start: 0.7159 (mttp) cc_final: 0.6924 (ttmt) REVERT: D 185 ARG cc_start: 0.7382 (mtm180) cc_final: 0.7069 (mtp180) REVERT: D 208 ASP cc_start: 0.7593 (m-30) cc_final: 0.7114 (p0) REVERT: D 256 LEU cc_start: 0.8089 (mp) cc_final: 0.7806 (mm) REVERT: D 293 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: D 311 GLU cc_start: 0.7802 (pt0) cc_final: 0.7570 (pm20) REVERT: D 326 ASP cc_start: 0.7448 (m-30) cc_final: 0.7186 (m-30) REVERT: D 339 PHE cc_start: 0.8528 (m-80) cc_final: 0.8199 (m-80) REVERT: D 348 ASP cc_start: 0.8055 (t0) cc_final: 0.7739 (m-30) REVERT: D 351 GLU cc_start: 0.8067 (tp30) cc_final: 0.7754 (mm-30) REVERT: D 455 GLU cc_start: 0.7146 (tt0) cc_final: 0.6887 (mt-10) REVERT: D 464 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: D 481 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8274 (ptmt) REVERT: D 493 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7904 (mm-30) outliers start: 38 outliers final: 22 residues processed: 218 average time/residue: 0.6637 time to fit residues: 156.5021 Evaluate side-chains 209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 110 optimal weight: 0.0370 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103864 restraints weight = 15311.145| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.97 r_work: 0.3021 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13897 Z= 0.118 Angle : 0.505 10.793 18816 Z= 0.262 Chirality : 0.047 0.243 2104 Planarity : 0.003 0.041 2442 Dihedral : 5.004 58.695 1954 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.53 % Allowed : 23.08 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1736 helix: 0.42 (0.26), residues: 400 sheet: -0.90 (0.24), residues: 398 loop : -0.62 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 314 TYR 0.016 0.001 TYR C 357 PHE 0.015 0.001 PHE D 360 TRP 0.005 0.001 TRP D 186 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13896) covalent geometry : angle 0.50490 / 0.26 (18814) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 0.31411 / 0.18 ( 2) hydrogen bonds : bond 0.03051 / 2.04 ( 338) hydrogen bonds : angle 4.96221 / 3.56 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.562 Fit side-chains REVERT: A 145 PHE cc_start: 0.8476 (t80) cc_final: 0.8201 (t80) REVERT: A 220 ASP cc_start: 0.8408 (t0) cc_final: 0.7970 (t0) REVERT: A 254 LYS cc_start: 0.7709 (mttt) cc_final: 0.6536 (mmmt) REVERT: A 258 GLU cc_start: 0.7704 (pm20) cc_final: 0.7277 (pt0) REVERT: A 263 GLU cc_start: 0.7671 (tt0) cc_final: 0.7193 (tp30) REVERT: A 276 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6069 (mtp) REVERT: A 348 GLU cc_start: 0.8295 (tp30) cc_final: 0.8033 (tp30) REVERT: A 383 GLN cc_start: 0.7849 (tt0) cc_final: 0.7551 (tp-100) REVERT: A 399 ASP cc_start: 0.8656 (t0) cc_final: 0.8418 (t70) REVERT: A 412 LYS cc_start: 0.8674 (tttp) cc_final: 0.7951 (tptt) REVERT: A 488 ASN cc_start: 0.8214 (t0) cc_final: 0.7764 (t0) REVERT: A 494 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.7059 (mmm160) REVERT: B 102 ARG cc_start: 0.8332 (mtm180) cc_final: 0.8044 (mtp180) REVERT: B 144 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: B 184 LYS cc_start: 0.7350 (mttm) cc_final: 0.6858 (mtpt) REVERT: B 270 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: B 320 ARG cc_start: 0.7666 (mmm160) cc_final: 0.6409 (tpp-160) REVERT: B 348 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: B 352 ASP cc_start: 0.7697 (t0) cc_final: 0.7378 (p0) REVERT: B 481 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7956 (ptmm) REVERT: B 517 LYS cc_start: 0.7669 (mttt) cc_final: 0.7210 (mtpm) REVERT: C 156 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7456 (mtt-85) REVERT: C 309 MET cc_start: 0.8844 (tpp) cc_final: 0.8525 (tpp) REVERT: C 354 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: C 365 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7462 (mttt) REVERT: C 412 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8171 (tptt) REVERT: C 431 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8032 (tt0) REVERT: C 494 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6808 (mmm-85) REVERT: D 102 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7891 (mtm180) REVERT: D 156 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7475 (mpt180) REVERT: D 184 LYS cc_start: 0.7163 (mttp) cc_final: 0.6826 (ttmt) REVERT: D 185 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6686 (mmm160) REVERT: D 208 ASP cc_start: 0.7592 (m-30) cc_final: 0.7155 (p0) REVERT: D 244 ILE cc_start: 0.8467 (tp) cc_final: 0.8093 (pt) REVERT: D 256 LEU cc_start: 0.8068 (mp) cc_final: 0.7804 (mm) REVERT: D 293 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5612 (tt0) REVERT: D 326 ASP cc_start: 0.7428 (m-30) cc_final: 0.7143 (m-30) REVERT: D 348 ASP cc_start: 0.8081 (t0) cc_final: 0.7767 (m-30) REVERT: D 351 GLU cc_start: 0.8025 (tp30) cc_final: 0.7779 (mm-30) REVERT: D 455 GLU cc_start: 0.7133 (tt0) cc_final: 0.6839 (mt-10) REVERT: D 464 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: D 481 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8270 (ptmt) REVERT: D 493 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7949 (mm-30) outliers start: 37 outliers final: 22 residues processed: 210 average time/residue: 0.6631 time to fit residues: 151.0626 Evaluate side-chains 210 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 128 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 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 = 0.3539 r_free = 0.3539 target = 0.137693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100029 restraints weight = 15364.133| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.97 r_work: 0.2957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13897 Z= 0.237 Angle : 0.591 10.189 18816 Z= 0.307 Chirality : 0.050 0.277 2104 Planarity : 0.004 0.043 2442 Dihedral : 5.365 58.008 1954 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.33 % Allowed : 22.88 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1736 helix: 0.07 (0.25), residues: 402 sheet: -1.06 (0.24), residues: 390 loop : -0.69 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 337 TYR 0.014 0.002 TYR C 357 PHE 0.016 0.002 PHE D 360 TRP 0.004 0.001 TRP C 185 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (13896) covalent geometry : angle 0.59126 / 0.31 (18814) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.51330 / 0.30 ( 2) hydrogen bonds : bond 0.03668 / 2.42 ( 338) hydrogen bonds : angle 5.25264 / 3.76 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.574 Fit side-chains REVERT: A 145 PHE cc_start: 0.8633 (t80) cc_final: 0.8368 (t80) REVERT: A 220 ASP cc_start: 0.8456 (t0) cc_final: 0.8013 (t0) REVERT: A 222 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7806 (mm-30) REVERT: A 254 LYS cc_start: 0.7778 (mttt) cc_final: 0.6552 (mmmt) REVERT: A 258 GLU cc_start: 0.7822 (pm20) cc_final: 0.7356 (pt0) REVERT: A 263 GLU cc_start: 0.7620 (tt0) cc_final: 0.7158 (tp30) REVERT: A 276 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6193 (mtp) REVERT: A 348 GLU cc_start: 0.8277 (tp30) cc_final: 0.8015 (tp30) REVERT: A 399 ASP cc_start: 0.8728 (t0) cc_final: 0.8463 (t70) REVERT: A 412 LYS cc_start: 0.8702 (tttp) cc_final: 0.8030 (tptt) REVERT: A 487 ASP cc_start: 0.7994 (m-30) cc_final: 0.7485 (t0) REVERT: A 494 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7071 (mmm160) REVERT: B 102 ARG cc_start: 0.8327 (mtm180) cc_final: 0.8016 (mtp180) REVERT: B 144 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: B 184 LYS cc_start: 0.7470 (mttm) cc_final: 0.6976 (mtpt) REVERT: B 280 MET cc_start: 0.6481 (mmm) cc_final: 0.5994 (mmt) REVERT: B 320 ARG cc_start: 0.7677 (mmm160) cc_final: 0.6449 (tpp-160) REVERT: B 348 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: B 352 ASP cc_start: 0.7720 (t0) cc_final: 0.7354 (p0) REVERT: B 481 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8191 (ptmt) REVERT: C 156 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7444 (mtt-85) REVERT: C 293 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.5615 (mtp) REVERT: C 309 MET cc_start: 0.8853 (tpp) cc_final: 0.8525 (tpp) REVERT: C 354 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: C 365 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7389 (mttt) REVERT: C 431 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8079 (tt0) REVERT: C 494 ARG cc_start: 0.7224 (mmm-85) cc_final: 0.6792 (mmm-85) REVERT: D 102 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7874 (mtm180) REVERT: D 109 ARG cc_start: 0.8238 (ptp-110) cc_final: 0.7803 (ttm-80) REVERT: D 156 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7448 (mmt-90) REVERT: D 184 LYS cc_start: 0.7224 (mttp) cc_final: 0.6887 (ttmt) REVERT: D 185 ARG cc_start: 0.7394 (mtm180) cc_final: 0.6613 (mmm160) REVERT: D 208 ASP cc_start: 0.7688 (m-30) cc_final: 0.7201 (p0) REVERT: D 226 MET cc_start: 0.9175 (mmm) cc_final: 0.8896 (mmp) REVERT: D 256 LEU cc_start: 0.8217 (mp) cc_final: 0.7948 (mm) REVERT: D 293 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5595 (tt0) REVERT: D 326 ASP cc_start: 0.7386 (m-30) cc_final: 0.7098 (m-30) REVERT: D 339 PHE cc_start: 0.8464 (m-80) cc_final: 0.8254 (m-80) REVERT: D 348 ASP cc_start: 0.8089 (t0) cc_final: 0.7764 (m-30) REVERT: D 351 GLU cc_start: 0.8035 (tp30) cc_final: 0.7695 (mm-30) REVERT: D 464 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 481 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8309 (ptmt) REVERT: D 493 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7856 (mm-30) outliers start: 34 outliers final: 20 residues processed: 203 average time/residue: 0.6772 time to fit residues: 149.1412 Evaluate side-chains 205 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103190 restraints weight = 15294.543| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.98 r_work: 0.3002 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13897 Z= 0.120 Angle : 0.518 11.801 18816 Z= 0.268 Chirality : 0.048 0.272 2104 Planarity : 0.004 0.045 2442 Dihedral : 5.143 59.010 1954 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.12 % Allowed : 23.42 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1736 helix: 0.31 (0.25), residues: 402 sheet: -0.95 (0.24), residues: 398 loop : -0.66 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 337 TYR 0.015 0.001 TYR C 357 PHE 0.015 0.001 PHE D 360 TRP 0.005 0.001 TRP B 186 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13896) covalent geometry : angle 0.51775 / 0.27 (18814) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 0.36547 / 0.21 ( 2) hydrogen bonds : bond 0.03088 / 2.05 ( 338) hydrogen bonds : angle 5.04980 / 3.62 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5332.06 seconds wall clock time: 91 minutes 28.22 seconds (5488.22 seconds total)