Starting phenix.real_space_refine on Mon Jun 9 20:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2x_44117/06_2025/9b2x_44117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2x_44117/06_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_44117/06_2025/9b2x_44117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2x_44117/06_2025/9b2x_44117.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2x_44117/06_2025/9b2x_44117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2x_44117/06_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-5710/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: 8.64, per 1000 atoms: 0.80 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=21, 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 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 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: 2.54 Conformation dependent library (CDL) restraints added in 2.7 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: 1.41 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: 3.87 Time building geometry restraints manager: 2.96 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: 6353 21.03 - 42.07: 427 42.07 - 63.10: 60 63.10 - 84.14: 6 84.14 - 105.17: 27 Dihedral angle restraints: 6873 sinusoidal: 2784 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 6870 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: 2.20 - 2.74: 748 2.74 - 3.28: 10257 3.28 - 3.82: 15851 3.82 - 4.36: 18681 4.36 - 4.90: 34538 Nonbonded interactions: 80075 Sorted by model distance: nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.200 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.200 3.040 nonbonded pdb=" ND2 ASN A 444 " pdb=" O ASN A 460 " model vdw 2.294 3.120 nonbonded pdb=" ND2 ASN B 444 " pdb=" O ASN B 460 " model vdw 2.295 3.120 ... (remaining 80070 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: 1.920 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.970 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- 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 11055 Z= 0.138 Angle : 0.646 17.258 15018 Z= 0.344 Chirality : 0.045 0.401 1821 Planarity : 0.005 0.090 1866 Dihedral : 15.742 105.171 4164 Min Nonbonded Distance : 2.199 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01370 ( 6) link_NAG-ASN : angle 8.24040 ( 18) hydrogen bonds : bond 0.21287 ( 468) hydrogen bonds : angle 6.72208 ( 1269) SS BOND : bond 0.00169 ( 21) SS BOND : angle 0.89170 ( 42) covalent geometry : bond 0.00285 (11028) covalent geometry : angle 0.57925 (14958) *********************** 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 : 1.414 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: 0.2358 time to fit residues: 52.2145 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 : 1.274 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.149895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117878 restraints weight = 21069.587| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.84 r_work: 0.3064 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11055 Z= 0.172 Angle : 0.711 15.728 15018 Z= 0.357 Chirality : 0.050 0.483 1821 Planarity : 0.005 0.092 1866 Dihedral : 9.313 54.644 1602 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.03 % Allowed : 5.37 % Favored : 93.60 % 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: -0.96 (0.23), residues: 1377 helix: 1.29 (0.27), residues: 438 sheet: -0.14 (0.26), residues: 360 loop : -2.60 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 52 HIS 0.001 0.001 HIS C 317 PHE 0.010 0.002 PHE C 137 TYR 0.014 0.002 TYR A 441 ARG 0.005 0.001 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01278 ( 6) link_NAG-ASN : angle 7.26848 ( 18) hydrogen bonds : bond 0.05251 ( 468) hydrogen bonds : angle 4.92967 ( 1269) SS BOND : bond 0.00324 ( 21) SS BOND : angle 1.74786 ( 42) covalent geometry : bond 0.00420 (11028) covalent geometry : angle 0.65965 (14958) *********************** 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 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.340 Fit side-chains REVERT: A 232 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 370 MET cc_start: 0.8390 (ttp) cc_final: 0.8168 (ttp) REVERT: A 427 LYS cc_start: 0.6772 (pttt) cc_final: 0.6287 (mmtt) REVERT: B 161 GLU cc_start: 0.7810 (pp20) cc_final: 0.7560 (mm-30) REVERT: B 232 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 427 LYS cc_start: 0.6629 (pttt) cc_final: 0.6059 (mmtt) REVERT: C 232 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 427 LYS cc_start: 0.6786 (pttt) cc_final: 0.6273 (mmtt) REVERT: C 509 PHE cc_start: 0.6584 (t80) cc_final: 0.6326 (t80) outliers start: 13 outliers final: 10 residues processed: 117 average time/residue: 0.2004 time to fit residues: 35.7627 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 : 1.284 ------------------------------------------------------------------------------- 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: 0.8980 chunk 132 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4018 r_free = 0.4018 target = 0.175843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146454 restraints weight = 15904.558| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.29 r_work: 0.3499 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11055 Z= 0.141 Angle : 0.641 14.127 15018 Z= 0.326 Chirality : 0.048 0.473 1821 Planarity : 0.005 0.087 1866 Dihedral : 6.729 49.060 1602 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.87 % Allowed : 6.87 % Favored : 92.26 % 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: -0.86 (0.23), residues: 1377 helix: 1.33 (0.27), residues: 438 sheet: 0.02 (0.26), residues: 360 loop : -2.57 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 52 HIS 0.001 0.001 HIS A 317 PHE 0.009 0.001 PHE C 137 TYR 0.012 0.001 TYR C 441 ARG 0.004 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01146 ( 6) link_NAG-ASN : angle 6.68032 ( 18) hydrogen bonds : bond 0.04557 ( 468) hydrogen bonds : angle 4.46861 ( 1269) SS BOND : bond 0.00281 ( 21) SS BOND : angle 1.41180 ( 42) covalent geometry : bond 0.00337 (11028) covalent geometry : angle 0.59422 (14958) *********************** 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 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8311 (t80) cc_final: 0.7898 (t80) REVERT: A 370 MET cc_start: 0.8537 (ttp) cc_final: 0.8204 (ttp) REVERT: A 427 LYS cc_start: 0.6938 (pttt) cc_final: 0.6443 (mptt) REVERT: B 232 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 251 MET cc_start: 0.8729 (mmm) cc_final: 0.8396 (mmm) REVERT: B 427 LYS cc_start: 0.6790 (pttt) cc_final: 0.6290 (mmtt) REVERT: C 232 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7408 (mm-30) REVERT: C 309 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7803 (mm) REVERT: C 509 PHE cc_start: 0.6626 (t80) cc_final: 0.6374 (t80) outliers start: 11 outliers final: 9 residues processed: 121 average time/residue: 0.2031 time to fit residues: 36.7829 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU 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 C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.173901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144195 restraints weight = 27448.631| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.93 r_work: 0.3378 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11055 Z= 0.167 Angle : 0.666 19.834 15018 Z= 0.336 Chirality : 0.048 0.461 1821 Planarity : 0.005 0.092 1866 Dihedral : 6.624 55.624 1602 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.42 % Allowed : 7.82 % Favored : 90.76 % 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: -0.96 (0.22), residues: 1377 helix: 1.25 (0.27), residues: 438 sheet: -0.11 (0.25), residues: 363 loop : -2.59 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 52 HIS 0.001 0.001 HIS C 317 PHE 0.010 0.001 PHE C 137 TYR 0.015 0.001 TYR B 441 ARG 0.003 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01367 ( 6) link_NAG-ASN : angle 7.48596 ( 18) hydrogen bonds : bond 0.04962 ( 468) hydrogen bonds : angle 4.49679 ( 1269) SS BOND : bond 0.00338 ( 21) SS BOND : angle 1.59280 ( 42) covalent geometry : bond 0.00412 (11028) covalent geometry : angle 0.60845 (14958) *********************** 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 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 207 VAL cc_start: 0.5518 (OUTLIER) cc_final: 0.5263 (m) REVERT: A 370 MET cc_start: 0.8630 (ttp) cc_final: 0.8323 (ttp) REVERT: A 427 LYS cc_start: 0.7063 (pttt) cc_final: 0.6493 (mptt) REVERT: B 232 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 363 ASN cc_start: 0.8182 (p0) cc_final: 0.7851 (p0) REVERT: B 427 LYS cc_start: 0.6902 (pttt) cc_final: 0.6321 (mmtt) REVERT: C 232 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7660 (mm-30) outliers start: 18 outliers final: 12 residues processed: 125 average time/residue: 0.1997 time to fit residues: 37.6294 Evaluate side-chains 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 A residue 357 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 110 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148398 restraints weight = 24315.695| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.83 r_work: 0.3437 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11055 Z= 0.117 Angle : 0.617 20.453 15018 Z= 0.307 Chirality : 0.045 0.432 1821 Planarity : 0.005 0.084 1866 Dihedral : 6.429 59.111 1602 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.03 % Allowed : 8.21 % Favored : 90.76 % 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: -0.71 (0.23), residues: 1377 helix: 1.50 (0.27), residues: 438 sheet: 0.09 (0.26), residues: 360 loop : -2.52 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.001 0.000 HIS A 317 PHE 0.006 0.001 PHE C 137 TYR 0.010 0.001 TYR B 299 ARG 0.002 0.000 ARG A 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01177 ( 6) link_NAG-ASN : angle 8.30637 ( 18) hydrogen bonds : bond 0.03751 ( 468) hydrogen bonds : angle 4.17626 ( 1269) SS BOND : bond 0.00245 ( 21) SS BOND : angle 1.18750 ( 42) covalent geometry : bond 0.00269 (11028) covalent geometry : angle 0.54370 (14958) *********************** 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 136 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8326 (t80) cc_final: 0.7951 (t80) REVERT: A 207 VAL cc_start: 0.5328 (OUTLIER) cc_final: 0.5055 (m) REVERT: A 235 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6161 (mmt180) REVERT: A 363 ASN cc_start: 0.8258 (p0) cc_final: 0.8047 (p0) REVERT: A 370 MET cc_start: 0.8591 (ttp) cc_final: 0.8369 (ttp) REVERT: A 421 LYS cc_start: 0.7451 (tttm) cc_final: 0.6991 (pptt) REVERT: A 427 LYS cc_start: 0.7013 (pttt) cc_final: 0.6469 (mptt) REVERT: B 232 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 235 ARG cc_start: 0.7055 (ttm170) cc_final: 0.5906 (mmt180) REVERT: B 427 LYS cc_start: 0.6831 (pttt) cc_final: 0.6275 (mmtt) REVERT: C 232 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7676 (mm-30) REVERT: C 235 ARG cc_start: 0.7164 (ttm170) cc_final: 0.6016 (mmt180) outliers start: 13 outliers final: 12 residues processed: 131 average time/residue: 0.2271 time to fit residues: 43.0841 Evaluate side-chains 132 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 A residue 357 THR 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 425 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: 4.9990 chunk 100 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 380 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143090 restraints weight = 22933.602| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.99 r_work: 0.3340 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11055 Z= 0.266 Angle : 0.753 18.531 15018 Z= 0.383 Chirality : 0.051 0.467 1821 Planarity : 0.006 0.090 1866 Dihedral : 6.507 50.101 1602 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.90 % Allowed : 8.53 % Favored : 89.57 % 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: -1.17 (0.22), residues: 1377 helix: 0.96 (0.26), residues: 435 sheet: -0.19 (0.25), residues: 363 loop : -2.62 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 52 HIS 0.002 0.001 HIS C 317 PHE 0.017 0.002 PHE C 137 TYR 0.020 0.002 TYR B 441 ARG 0.004 0.001 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 6) link_NAG-ASN : angle 7.70730 ( 18) hydrogen bonds : bond 0.06383 ( 468) hydrogen bonds : angle 4.73702 ( 1269) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.91019 ( 42) covalent geometry : bond 0.00686 (11028) covalent geometry : angle 0.69864 (14958) *********************** 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 131 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.353 Fit side-chains REVERT: A 207 VAL cc_start: 0.5503 (OUTLIER) cc_final: 0.5258 (m) REVERT: A 370 MET cc_start: 0.8695 (ttp) cc_final: 0.8415 (ttp) REVERT: B 427 LYS cc_start: 0.6910 (pttt) cc_final: 0.6325 (mmtt) REVERT: C 202 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7656 (mm-40) REVERT: C 232 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7614 (mm-30) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.2195 time to fit residues: 40.4074 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 384 VAL 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 Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146662 restraints weight = 25181.689| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.30 r_work: 0.3412 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- 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 = 0.46 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: 0.8056 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11055 Z= 0.134 Angle : 0.644 22.144 15018 Z= 0.319 Chirality : 0.046 0.474 1821 Planarity : 0.005 0.082 1866 Dihedral : 6.700 58.976 1602 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.03 % Allowed : 9.56 % Favored : 89.42 % 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: -0.90 (0.22), residues: 1377 helix: 1.28 (0.27), residues: 438 sheet: -0.07 (0.25), residues: 363 loop : -2.54 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 314 HIS 0.002 0.001 HIS A 317 PHE 0.007 0.001 PHE A 137 TYR 0.011 0.001 TYR C 299 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01244 ( 6) link_NAG-ASN : angle 9.02171 ( 18) hydrogen bonds : bond 0.04250 ( 468) hydrogen bonds : angle 4.26942 ( 1269) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.21550 ( 42) covalent geometry : bond 0.00316 (11028) covalent geometry : angle 0.56095 (14958) *********************** 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 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.220 Fit side-chains REVERT: A 198 TYR cc_start: 0.8357 (t80) cc_final: 0.7957 (t80) REVERT: A 235 ARG cc_start: 0.7306 (ttm170) cc_final: 0.6246 (mmt180) REVERT: A 427 LYS cc_start: 0.7040 (pttt) cc_final: 0.6502 (mptt) REVERT: B 92 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7622 (tt0) REVERT: B 235 ARG cc_start: 0.7231 (ttm170) cc_final: 0.6068 (mmt180) REVERT: B 427 LYS cc_start: 0.6841 (pttt) cc_final: 0.6257 (mmtt) REVERT: C 232 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7640 (mm-30) outliers start: 13 outliers final: 12 residues processed: 122 average time/residue: 0.2243 time to fit residues: 40.1327 Evaluate side-chains 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 A residue 357 THR 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 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: 0.0770 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.177335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148613 restraints weight = 22789.650| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.64 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11055 Z= 0.117 Angle : 0.601 19.070 15018 Z= 0.300 Chirality : 0.045 0.450 1821 Planarity : 0.005 0.082 1866 Dihedral : 6.029 55.836 1602 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.71 % Allowed : 10.03 % Favored : 89.26 % 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: -0.71 (0.23), residues: 1377 helix: 1.45 (0.27), residues: 438 sheet: 0.12 (0.25), residues: 360 loop : -2.49 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.001 0.000 HIS A 317 PHE 0.006 0.001 PHE C 137 TYR 0.010 0.001 TYR B 299 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01256 ( 6) link_NAG-ASN : angle 7.95417 ( 18) hydrogen bonds : bond 0.03532 ( 468) hydrogen bonds : angle 4.03900 ( 1269) SS BOND : bond 0.00253 ( 21) SS BOND : angle 1.09834 ( 42) covalent geometry : bond 0.00271 (11028) covalent geometry : angle 0.53173 (14958) *********************** 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 129 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.218 Fit side-chains REVERT: A 198 TYR cc_start: 0.8378 (t80) cc_final: 0.8134 (t80) REVERT: A 235 ARG cc_start: 0.6530 (ttm170) cc_final: 0.6252 (mmt180) REVERT: A 427 LYS cc_start: 0.6746 (pttt) cc_final: 0.6419 (mptt) REVERT: B 92 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7435 (tt0) REVERT: B 235 ARG cc_start: 0.6326 (ttm170) cc_final: 0.5865 (mmt180) REVERT: B 427 LYS cc_start: 0.6548 (pttt) cc_final: 0.6178 (mmtt) REVERT: C 235 ARG cc_start: 0.6497 (ttm170) cc_final: 0.5822 (mmt180) outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.2325 time to fit residues: 41.2956 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 371 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 = 0.4024 r_free = 0.4024 target = 0.176202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147309 restraints weight = 29315.376| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.20 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11055 Z= 0.133 Angle : 0.613 18.865 15018 Z= 0.309 Chirality : 0.046 0.452 1821 Planarity : 0.005 0.079 1866 Dihedral : 5.747 54.827 1596 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.71 % Allowed : 10.35 % 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: -0.70 (0.23), residues: 1377 helix: 1.44 (0.27), residues: 438 sheet: 0.12 (0.25), residues: 360 loop : -2.46 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.001 0.000 HIS C 317 PHE 0.007 0.001 PHE C 137 TYR 0.012 0.001 TYR C 441 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01306 ( 6) link_NAG-ASN : angle 7.53706 ( 18) hydrogen bonds : bond 0.03974 ( 468) hydrogen bonds : angle 4.13468 ( 1269) SS BOND : bond 0.00262 ( 21) SS BOND : angle 1.48071 ( 42) covalent geometry : bond 0.00318 (11028) covalent geometry : angle 0.55011 (14958) *********************** 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 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.227 Fit side-chains REVERT: A 198 TYR cc_start: 0.8395 (t80) cc_final: 0.8138 (t80) REVERT: A 235 ARG cc_start: 0.6645 (ttm170) cc_final: 0.6375 (mmt180) REVERT: A 427 LYS cc_start: 0.6709 (pttt) cc_final: 0.6373 (mptt) REVERT: B 92 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7462 (tt0) REVERT: B 235 ARG cc_start: 0.6465 (ttm170) cc_final: 0.6003 (mmt180) REVERT: C 235 ARG cc_start: 0.6572 (ttm170) cc_final: 0.6289 (mmt180) outliers start: 9 outliers final: 9 residues processed: 114 average time/residue: 0.2403 time to fit residues: 39.4667 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 377 SER 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 1 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 9 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.178500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150911 restraints weight = 21693.756| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.45 r_work: 0.3479 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11055 Z= 0.112 Angle : 0.575 17.878 15018 Z= 0.291 Chirality : 0.045 0.443 1821 Planarity : 0.005 0.080 1866 Dihedral : 5.619 54.863 1596 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.47 % Allowed : 10.74 % Favored : 88.78 % 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: -0.53 (0.23), residues: 1377 helix: 1.59 (0.27), residues: 438 sheet: 0.21 (0.25), residues: 360 loop : -2.38 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.001 0.000 HIS B 317 PHE 0.006 0.001 PHE B 351 TYR 0.010 0.001 TYR C 299 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01300 ( 6) link_NAG-ASN : angle 7.05381 ( 18) hydrogen bonds : bond 0.03394 ( 468) hydrogen bonds : angle 3.98342 ( 1269) SS BOND : bond 0.00225 ( 21) SS BOND : angle 1.27340 ( 42) covalent geometry : bond 0.00255 (11028) covalent geometry : angle 0.51743 (14958) ********************** 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: 6 poor density : 114 time to evaluate : 1.298 Fit side-chains REVERT: A 198 TYR cc_start: 0.8318 (t80) cc_final: 0.8035 (t80) REVERT: A 235 ARG cc_start: 0.7254 (ttm170) cc_final: 0.6214 (mmt180) REVERT: A 427 LYS cc_start: 0.7078 (pttt) cc_final: 0.6529 (mptt) REVERT: B 92 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7696 (tt0) REVERT: B 235 ARG cc_start: 0.7073 (ttm170) cc_final: 0.5935 (mmt180) REVERT: C 235 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6019 (mmt180) outliers start: 6 outliers final: 6 residues processed: 116 average time/residue: 0.2404 time to fit residues: 40.4920 Evaluate side-chains 118 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 169 SER 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: 0.0770 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 0.0370 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 428 ASN B 159 HIS B 428 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 = 0.4085 r_free = 0.4085 target = 0.183176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154646 restraints weight = 23843.017| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.75 r_work: 0.3496 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11055 Z= 0.097 Angle : 0.539 16.802 15018 Z= 0.275 Chirality : 0.044 0.424 1821 Planarity : 0.004 0.082 1866 Dihedral : 5.478 55.730 1596 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.47 % Allowed : 10.82 % 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: -0.27 (0.23), residues: 1377 helix: 1.82 (0.27), residues: 441 sheet: 0.32 (0.25), residues: 357 loop : -2.20 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 314 HIS 0.001 0.000 HIS C 317 PHE 0.004 0.001 PHE B 509 TYR 0.009 0.001 TYR B 299 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01302 ( 6) link_NAG-ASN : angle 6.54415 ( 18) hydrogen bonds : bond 0.02561 ( 468) hydrogen bonds : angle 3.73157 ( 1269) SS BOND : bond 0.00171 ( 21) SS BOND : angle 0.88374 ( 42) covalent geometry : bond 0.00209 (11028) covalent geometry : angle 0.48746 (14958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5015.36 seconds wall clock time: 87 minutes 1.86 seconds (5221.86 seconds total)