Starting phenix.real_space_refine on Fri Jan 17 14:35:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2x_44117/01_2025/9b2x_44117_neut.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6876 2.51 5 N 1788 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10860 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 462, 3583 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 462, 3583 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 1 bond proxies already assigned to first conformer: 3626 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 8.76, per 1000 atoms: 0.81 Number of scatterers: 10860 At special positions: 0 Unit cell: (90.09, 94.64, 143.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2133 8.00 N 1788 7.00 C 6876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 27 " " NAG A 602 " - " ASN A 500 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 500 " " NAG C 601 " - " ASN C 27 " " NAG C 602 " - " ASN C 500 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 3.1 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 18 sheets defined 33.3% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 73 through 98 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 207 removed outlier: 4.695A pdb=" N LEU A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 216 through 240 removed outlier: 3.718A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.711A pdb=" N LEU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.749A pdb=" N VAL A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.575A pdb=" N VAL A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 382 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 383 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.629A pdb=" N ASN A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 517 removed outlier: 3.552A pdb=" N GLN A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 98 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 207 removed outlier: 4.695A pdb=" N LEU B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 216 through 240 removed outlier: 3.719A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.711A pdb=" N LEU B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.750A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.576A pdb=" N VAL B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 382 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.628A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 517 removed outlier: 3.552A pdb=" N GLN B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 207 removed outlier: 4.695A pdb=" N LEU C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 216 through 240 removed outlier: 3.718A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.711A pdb=" N LEU C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.749A pdb=" N VAL C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 383 removed outlier: 3.575A pdb=" N VAL C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 382 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 383 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.628A pdb=" N ASN C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 517 removed outlier: 3.553A pdb=" N GLN C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 503 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 504 " --> pdb=" O ASN C 500 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.597A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.597A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 38 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 3.857A pdb=" N ALA A 177 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 11.923A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 287 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 434 removed outlier: 7.025A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.596A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.596A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 38 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 3.856A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 11.923A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 287 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'B' and resid 431 through 434 removed outlier: 7.023A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 359 through 361 removed outlier: 8.596A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 359 through 361 removed outlier: 8.596A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 38 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.857A pdb=" N ALA C 177 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 287 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'C' and resid 431 through 434 removed outlier: 7.023A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3453 1.34 - 1.47: 2447 1.47 - 1.59: 5044 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 11028 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.57e+00 bond pdb=" C THR A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" C THR C 245 " pdb=" N PRO C 246 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.50e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 11023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 14349 1.29 - 2.58: 508 2.58 - 3.86: 74 3.86 - 5.15: 15 5.15 - 6.44: 12 Bond angle restraints: 14958 Sorted by residual: angle pdb=" C GLN B 361 " pdb=" N SER B 362 " pdb=" CA SER B 362 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C GLN A 361 " pdb=" N SER A 362 " pdb=" CA SER A 362 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.60e+00 angle pdb=" C GLN C 361 " pdb=" N SER C 362 " pdb=" CA SER C 362 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.57e+00 angle pdb=" C THR B 245 " pdb=" CA THR B 245 " pdb=" CB THR B 245 " ideal model delta sigma weight residual 110.17 115.76 -5.59 1.97e+00 2.58e-01 8.04e+00 angle pdb=" C THR A 245 " pdb=" CA THR A 245 " pdb=" CB THR A 245 " ideal model delta sigma weight residual 110.17 115.74 -5.57 1.97e+00 2.58e-01 8.00e+00 ... (remaining 14953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 6327 21.03 - 42.07: 411 42.07 - 63.10: 60 63.10 - 84.14: 6 84.14 - 105.17: 27 Dihedral angle restraints: 6831 sinusoidal: 2742 harmonic: 4089 Sorted by residual: dihedral pdb=" CA THR B 245 " pdb=" C THR B 245 " pdb=" N PRO B 246 " pdb=" CA PRO B 246 " ideal model delta harmonic sigma weight residual -180.00 -133.30 -46.70 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA THR C 245 " pdb=" C THR C 245 " pdb=" N PRO C 246 " pdb=" CA PRO C 246 " ideal model delta harmonic sigma weight residual 180.00 -133.36 -46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA THR A 245 " pdb=" C THR A 245 " pdb=" N PRO A 246 " pdb=" CA PRO A 246 " ideal model delta harmonic sigma weight residual -180.00 -133.37 -46.63 0 5.00e+00 4.00e-02 8.70e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1663 0.080 - 0.161: 154 0.161 - 0.241: 1 0.241 - 0.321: 0 0.321 - 0.401: 3 Chirality restraints: 1821 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 1818 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 245 " 0.059 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO C 246 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 246 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 246 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 245 " 0.059 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO A 246 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 245 " 0.058 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO B 246 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " 0.050 5.00e-02 4.00e+02 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 86 2.60 - 3.18: 8940 3.18 - 3.75: 14601 3.75 - 4.33: 20409 4.33 - 4.90: 36081 Nonbonded interactions: 80117 Sorted by model distance: nonbonded pdb=" SG CYS B 322 " pdb=" SG CYS B 333 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 322 " pdb=" SG CYS C 333 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 358 " pdb=" SG CYS B 367 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 69 " pdb=" SG CYS B 212 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 69 " pdb=" SG CYS C 212 " model vdw 2.030 3.760 ... (remaining 80112 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=0.50 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: 2.950 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 32.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.003 0.038 11028 Z= 0.183 Angle : 0.579 6.439 14958 Z= 0.331 Chirality : 0.045 0.401 1821 Planarity : 0.005 0.090 1866 Dihedral : 15.742 105.171 4164 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.47 % Allowed : 0.32 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1377 helix: 1.24 (0.27), residues: 447 sheet: -0.13 (0.27), residues: 342 loop : -2.72 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 52 HIS 0.002 0.001 HIS A 514 PHE 0.015 0.001 PHE B 237 TYR 0.013 0.001 TYR A 441 ARG 0.012 0.001 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.259 Fit side-chains REVERT: A 198 TYR cc_start: 0.8216 (t80) cc_final: 0.7952 (t80) REVERT: A 232 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6699 (mm-30) REVERT: A 235 ARG cc_start: 0.6324 (ttm170) cc_final: 0.5687 (mmt180) REVERT: A 370 MET cc_start: 0.8568 (ttp) cc_final: 0.8303 (ttp) REVERT: A 427 LYS cc_start: 0.6389 (pttt) cc_final: 0.5935 (mmtt) REVERT: B 235 ARG cc_start: 0.6264 (ttm170) cc_final: 0.5545 (mmt180) REVERT: B 427 LYS cc_start: 0.6520 (pttt) cc_final: 0.6196 (mmtt) REVERT: C 198 TYR cc_start: 0.8218 (t80) cc_final: 0.8010 (t80) REVERT: C 232 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6940 (mm-30) REVERT: C 235 ARG cc_start: 0.6343 (ttm170) cc_final: 0.5841 (mmt180) REVERT: C 427 LYS cc_start: 0.6574 (pttt) cc_final: 0.6137 (mmtt) REVERT: C 509 PHE cc_start: 0.6467 (t80) cc_final: 0.6222 (t80) outliers start: 6 outliers final: 3 residues processed: 155 average time/residue: 0.2333 time to fit residues: 51.9214 Evaluate side-chains 112 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 428 ASN B 227 ASN B 262 ASN B 380 ASN B 428 ASN C 262 ASN C 302 GLN C 380 ASN C 428 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115532 restraints weight = 21160.637| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.98 r_work: 0.3080 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11028 Z= 0.282 Angle : 0.667 8.970 14958 Z= 0.348 Chirality : 0.050 0.487 1821 Planarity : 0.005 0.092 1866 Dihedral : 9.270 54.042 1602 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.18 % Allowed : 5.06 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1377 helix: 1.28 (0.27), residues: 438 sheet: -0.08 (0.26), residues: 360 loop : -2.60 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 341 HIS 0.001 0.001 HIS C 317 PHE 0.010 0.002 PHE C 137 TYR 0.015 0.002 TYR A 441 ARG 0.005 0.001 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.320 Fit side-chains REVERT: A 232 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 370 MET cc_start: 0.8385 (ttp) cc_final: 0.8149 (ttp) REVERT: A 427 LYS cc_start: 0.6788 (pttt) cc_final: 0.6296 (mmtt) REVERT: B 161 GLU cc_start: 0.7771 (pp20) cc_final: 0.7550 (mm-30) REVERT: B 232 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 427 LYS cc_start: 0.6629 (pttt) cc_final: 0.6077 (mmtt) REVERT: C 232 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 427 LYS cc_start: 0.6813 (pttt) cc_final: 0.6295 (mmtt) REVERT: C 509 PHE cc_start: 0.6525 (t80) cc_final: 0.6282 (t80) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.2057 time to fit residues: 37.7577 Evaluate side-chains 109 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN B 380 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144370 restraints weight = 16087.545| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.25 r_work: 0.3422 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11028 Z= 0.399 Angle : 0.703 9.567 14958 Z= 0.371 Chirality : 0.052 0.488 1821 Planarity : 0.006 0.094 1866 Dihedral : 7.042 47.265 1602 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.18 % Allowed : 7.66 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1377 helix: 0.70 (0.26), residues: 453 sheet: -0.19 (0.26), residues: 363 loop : -2.67 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 52 HIS 0.002 0.001 HIS A 317 PHE 0.015 0.002 PHE C 137 TYR 0.018 0.002 TYR B 441 ARG 0.003 0.001 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8685 (ttp) cc_final: 0.8368 (ttp) REVERT: B 427 LYS cc_start: 0.6904 (pttt) cc_final: 0.6376 (mmtt) REVERT: C 202 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7615 (mm-40) REVERT: C 232 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7559 (mm-30) outliers start: 15 outliers final: 13 residues processed: 118 average time/residue: 0.1930 time to fit residues: 34.7269 Evaluate side-chains 115 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 0.0020 chunk 40 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147844 restraints weight = 27426.899| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.95 r_work: 0.3418 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11028 Z= 0.174 Angle : 0.553 7.551 14958 Z= 0.296 Chirality : 0.045 0.459 1821 Planarity : 0.005 0.085 1866 Dihedral : 6.777 57.093 1602 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.95 % Allowed : 8.06 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1377 helix: 1.38 (0.27), residues: 438 sheet: 0.02 (0.26), residues: 363 loop : -2.54 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.002 0.001 HIS A 317 PHE 0.006 0.001 PHE B 509 TYR 0.010 0.001 TYR C 299 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8325 (t80) cc_final: 0.7881 (t80) REVERT: A 207 VAL cc_start: 0.5421 (OUTLIER) cc_final: 0.5148 (m) REVERT: A 235 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6166 (mmt180) REVERT: A 370 MET cc_start: 0.8581 (ttp) cc_final: 0.8300 (ttp) REVERT: A 427 LYS cc_start: 0.7001 (pttt) cc_final: 0.6405 (mptt) REVERT: B 427 LYS cc_start: 0.6904 (pttt) cc_final: 0.6304 (mmtt) REVERT: C 232 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7665 (mm-30) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2339 time to fit residues: 44.8206 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 104 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 110 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 428 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150077 restraints weight = 24461.536| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.72 r_work: 0.3437 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11028 Z= 0.161 Angle : 0.530 7.757 14958 Z= 0.283 Chirality : 0.045 0.422 1821 Planarity : 0.005 0.088 1866 Dihedral : 6.244 52.429 1602 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.79 % Allowed : 8.77 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1377 helix: 1.48 (0.27), residues: 438 sheet: 0.25 (0.26), residues: 360 loop : -2.46 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.001 0.000 HIS A 317 PHE 0.005 0.001 PHE C 137 TYR 0.011 0.001 TYR C 299 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8302 (t80) cc_final: 0.7946 (t80) REVERT: A 207 VAL cc_start: 0.5324 (OUTLIER) cc_final: 0.5068 (m) REVERT: A 235 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6154 (mmt180) REVERT: A 370 MET cc_start: 0.8601 (ttp) cc_final: 0.8325 (ttp) REVERT: A 421 LYS cc_start: 0.7446 (tttp) cc_final: 0.6984 (pptt) REVERT: A 427 LYS cc_start: 0.6936 (pttt) cc_final: 0.6422 (mptt) REVERT: B 235 ARG cc_start: 0.7067 (ttm170) cc_final: 0.5848 (mmt180) REVERT: C 232 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7689 (mm-30) REVERT: C 235 ARG cc_start: 0.7205 (ttm170) cc_final: 0.5907 (mmt180) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.2273 time to fit residues: 44.2686 Evaluate side-chains 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 428 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.172095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143543 restraints weight = 23022.201| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.60 r_work: 0.3394 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11028 Z= 0.325 Angle : 0.622 8.933 14958 Z= 0.330 Chirality : 0.049 0.459 1821 Planarity : 0.005 0.092 1866 Dihedral : 6.253 49.798 1600 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.12 % Rotamer: Outliers : 1.18 % Allowed : 9.48 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1377 helix: 1.17 (0.26), residues: 438 sheet: 0.00 (0.26), residues: 363 loop : -2.55 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.002 0.001 HIS C 317 PHE 0.012 0.001 PHE C 137 TYR 0.017 0.002 TYR B 441 ARG 0.003 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.182 Fit side-chains REVERT: A 207 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.5041 (m) REVERT: A 235 ARG cc_start: 0.7438 (ttm170) cc_final: 0.6378 (mmt180) REVERT: A 370 MET cc_start: 0.8660 (ttp) cc_final: 0.8386 (ttp) REVERT: A 427 LYS cc_start: 0.7048 (pttt) cc_final: 0.6557 (mptt) REVERT: C 92 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7878 (tt0) REVERT: C 232 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7684 (mm-30) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.2408 time to fit residues: 41.7515 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.0000 chunk 133 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.176791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148528 restraints weight = 25239.961| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.82 r_work: 0.3435 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11028 Z= 0.170 Angle : 0.532 7.591 14958 Z= 0.285 Chirality : 0.045 0.463 1821 Planarity : 0.005 0.083 1866 Dihedral : 6.542 59.908 1600 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.63 % Allowed : 10.35 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1377 helix: 1.47 (0.27), residues: 438 sheet: 0.18 (0.26), residues: 360 loop : -2.46 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.001 0.001 HIS A 317 PHE 0.006 0.001 PHE C 137 TYR 0.010 0.001 TYR C 299 ARG 0.002 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.268 Fit side-chains REVERT: A 198 TYR cc_start: 0.8319 (t80) cc_final: 0.7979 (t80) REVERT: A 235 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6148 (mmt180) REVERT: A 370 MET cc_start: 0.8604 (ttp) cc_final: 0.8332 (ttp) REVERT: A 417 TYR cc_start: 0.8345 (m-80) cc_final: 0.8136 (m-80) REVERT: A 421 LYS cc_start: 0.7421 (tttp) cc_final: 0.6972 (pptt) REVERT: A 427 LYS cc_start: 0.6992 (pttt) cc_final: 0.6415 (mptt) REVERT: B 235 ARG cc_start: 0.7092 (ttm170) cc_final: 0.5902 (mmt180) REVERT: C 92 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7910 (tt0) REVERT: C 232 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7651 (mm-30) REVERT: C 235 ARG cc_start: 0.7180 (ttm170) cc_final: 0.5976 (mmt180) outliers start: 8 outliers final: 8 residues processed: 117 average time/residue: 0.2473 time to fit residues: 41.3243 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137124 restraints weight = 22613.653| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.17 r_work: 0.3399 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11028 Z= 0.233 Angle : 0.562 8.130 14958 Z= 0.299 Chirality : 0.046 0.465 1821 Planarity : 0.005 0.085 1866 Dihedral : 5.920 55.374 1596 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.79 % Allowed : 10.27 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1377 helix: 1.38 (0.27), residues: 438 sheet: 0.10 (0.26), residues: 363 loop : -2.44 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.001 0.000 HIS C 317 PHE 0.008 0.001 PHE A 137 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.263 Fit side-chains REVERT: A 198 TYR cc_start: 0.8236 (t80) cc_final: 0.7868 (t80) REVERT: A 235 ARG cc_start: 0.7083 (ttm170) cc_final: 0.5986 (mmt180) REVERT: A 370 MET cc_start: 0.8574 (ttp) cc_final: 0.8302 (ttp) REVERT: A 427 LYS cc_start: 0.7054 (pttt) cc_final: 0.6444 (mptt) REVERT: B 235 ARG cc_start: 0.6963 (ttm170) cc_final: 0.5800 (mmt180) REVERT: C 92 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7837 (tt0) REVERT: C 232 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 235 ARG cc_start: 0.6922 (ttm170) cc_final: 0.5793 (mmt180) REVERT: C 309 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (mm) outliers start: 10 outliers final: 9 residues processed: 116 average time/residue: 0.2379 time to fit residues: 40.1719 Evaluate side-chains 119 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140246 restraints weight = 29651.619| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.35 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11028 Z= 0.379 Angle : 0.650 9.156 14958 Z= 0.346 Chirality : 0.050 0.490 1821 Planarity : 0.005 0.082 1866 Dihedral : 6.076 52.512 1596 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.03 % Allowed : 10.58 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1377 helix: 1.09 (0.26), residues: 435 sheet: -0.09 (0.26), residues: 363 loop : -2.50 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 52 HIS 0.002 0.001 HIS B 159 PHE 0.014 0.002 PHE C 137 TYR 0.017 0.002 TYR B 441 ARG 0.003 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.153 Fit side-chains REVERT: A 235 ARG cc_start: 0.6815 (ttm170) cc_final: 0.6530 (mmt180) REVERT: A 427 LYS cc_start: 0.6700 (pttt) cc_final: 0.6430 (mmtt) REVERT: A 431 ILE cc_start: 0.8486 (mm) cc_final: 0.8278 (mt) REVERT: C 431 ILE cc_start: 0.8471 (mm) cc_final: 0.7906 (tt) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.2300 time to fit residues: 37.0481 Evaluate side-chains 116 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147320 restraints weight = 21890.503| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.53 r_work: 0.3402 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11028 Z= 0.215 Angle : 0.553 7.777 14958 Z= 0.297 Chirality : 0.047 0.463 1821 Planarity : 0.005 0.081 1866 Dihedral : 5.934 54.399 1596 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.71 % Allowed : 10.58 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1377 helix: 1.31 (0.26), residues: 438 sheet: 0.04 (0.26), residues: 363 loop : -2.45 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 314 HIS 0.002 0.001 HIS C 317 PHE 0.013 0.001 PHE B 509 TYR 0.011 0.001 TYR C 299 ARG 0.002 0.000 ARG C 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.167 Fit side-chains REVERT: A 198 TYR cc_start: 0.8358 (t80) cc_final: 0.7989 (t80) REVERT: A 235 ARG cc_start: 0.7353 (ttm170) cc_final: 0.6285 (mmt180) REVERT: B 235 ARG cc_start: 0.7281 (ttm170) cc_final: 0.6165 (mmt180) REVERT: C 235 ARG cc_start: 0.7251 (ttm170) cc_final: 0.6215 (mmt180) REVERT: C 431 ILE cc_start: 0.8373 (mm) cc_final: 0.7782 (tt) outliers start: 9 outliers final: 9 residues processed: 115 average time/residue: 0.2410 time to fit residues: 39.8364 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146830 restraints weight = 24041.005| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.66 r_work: 0.3420 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11028 Z= 0.224 Angle : 0.555 7.969 14958 Z= 0.297 Chirality : 0.047 0.433 1821 Planarity : 0.005 0.080 1866 Dihedral : 5.759 52.335 1596 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.79 % Allowed : 10.90 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1377 helix: 1.50 (0.27), residues: 429 sheet: 0.04 (0.26), residues: 363 loop : -2.43 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 314 HIS 0.001 0.001 HIS B 317 PHE 0.014 0.001 PHE B 509 TYR 0.012 0.001 TYR C 441 ARG 0.002 0.000 ARG C 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4738.54 seconds wall clock time: 85 minutes 51.72 seconds (5151.72 seconds total)