Starting phenix.real_space_refine on Tue May 13 19:56:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2x_44117/05_2025/9b2x_44117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2x_44117/05_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_44117/05_2025/9b2x_44117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2x_44117/05_2025/9b2x_44117.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2x_44117/05_2025/9b2x_44117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2x_44117/05_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-5687/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: 8.22, per 1000 atoms: 0.76 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: 2.25 Conformation dependent library (CDL) restraints added in 2.4 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: 1.36 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: 3.29 Time building geometry restraints manager: 2.69 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: 2.680 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.350 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- 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 : 1.373 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: 0.2245 time to fit residues: 49.9068 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 : 1.117 ------------------------------------------------------------------------------- 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 = 0.149882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117819 restraints weight = 21069.787| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.84 r_work: 0.3050 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 54.641 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 7.26862 ( 18) hydrogen bonds : bond 0.05251 ( 468) hydrogen bonds : angle 4.92964 ( 1269) SS BOND : bond 0.00323 ( 21) SS BOND : angle 1.74789 ( 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 : 1.119 Fit side-chains REVERT: A 232 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 370 MET cc_start: 0.8383 (ttp) cc_final: 0.8162 (ttp) REVERT: A 427 LYS cc_start: 0.6769 (pttt) cc_final: 0.6282 (mmtt) REVERT: B 161 GLU cc_start: 0.7801 (pp20) cc_final: 0.7553 (mm-30) REVERT: B 232 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 427 LYS cc_start: 0.6629 (pttt) cc_final: 0.6057 (mmtt) REVERT: C 232 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 427 LYS cc_start: 0.6782 (pttt) cc_final: 0.6264 (mmtt) REVERT: C 509 PHE cc_start: 0.6576 (t80) cc_final: 0.6320 (t80) outliers start: 13 outliers final: 10 residues processed: 117 average time/residue: 0.1981 time to fit residues: 35.0579 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 : 1.266 ------------------------------------------------------------------------------- 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: 0.2980 chunk 132 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.173799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145820 restraints weight = 15724.101| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.14 r_work: 0.3536 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11055 Z= 0.133 Angle : 0.630 14.132 15018 Z= 0.320 Chirality : 0.048 0.473 1821 Planarity : 0.005 0.086 1866 Dihedral : 6.691 49.668 1602 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.79 % Allowed : 6.95 % 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: -0.81 (0.23), residues: 1377 helix: 1.38 (0.27), residues: 438 sheet: 0.05 (0.26), residues: 360 loop : -2.55 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.001 0.001 HIS A 317 PHE 0.008 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 0.01189 ( 6) link_NAG-ASN : angle 6.70526 ( 18) hydrogen bonds : bond 0.04350 ( 468) hydrogen bonds : angle 4.43359 ( 1269) SS BOND : bond 0.00260 ( 21) SS BOND : angle 1.30997 ( 42) covalent geometry : bond 0.00310 (11028) covalent geometry : angle 0.58287 (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: 10 poor density : 118 time to evaluate : 1.203 Fit side-chains REVERT: A 198 TYR cc_start: 0.8230 (t80) cc_final: 0.7824 (t80) REVERT: A 370 MET cc_start: 0.8527 (ttp) cc_final: 0.8192 (ttp) REVERT: A 427 LYS cc_start: 0.6906 (pttt) cc_final: 0.6384 (mptt) REVERT: B 232 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7271 (mm-30) REVERT: B 251 MET cc_start: 0.8716 (mmm) cc_final: 0.8395 (mmm) REVERT: B 427 LYS cc_start: 0.6725 (pttt) cc_final: 0.6241 (mmtt) REVERT: C 232 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 509 PHE cc_start: 0.6489 (t80) cc_final: 0.6252 (t80) outliers start: 10 outliers final: 9 residues processed: 122 average time/residue: 0.1979 time to fit residues: 36.1248 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 0.3980 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: 2.9990 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.171555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141244 restraints weight = 27412.408| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.02 r_work: 0.3394 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11055 Z= 0.213 Angle : 0.722 21.668 15018 Z= 0.365 Chirality : 0.050 0.467 1821 Planarity : 0.006 0.096 1866 Dihedral : 6.778 54.555 1602 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.95 % Favored : 90.90 % Rotamer: Outliers : 1.58 % Allowed : 7.42 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1377 helix: 1.11 (0.26), residues: 435 sheet: -0.20 (0.25), residues: 363 loop : -2.57 (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 0.013 0.002 PHE C 137 TYR 0.018 0.002 TYR B 441 ARG 0.004 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01235 ( 6) link_NAG-ASN : angle 7.81289 ( 18) hydrogen bonds : bond 0.05868 ( 468) hydrogen bonds : angle 4.71357 ( 1269) SS BOND : bond 0.00386 ( 21) SS BOND : angle 1.87495 ( 42) covalent geometry : bond 0.00538 (11028) covalent geometry : angle 0.66293 (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 131 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.351 Fit side-chains REVERT: A 207 VAL cc_start: 0.5415 (OUTLIER) cc_final: 0.5198 (m) REVERT: A 370 MET cc_start: 0.8638 (ttp) cc_final: 0.8315 (ttp) REVERT: B 427 LYS cc_start: 0.6955 (pttt) cc_final: 0.6354 (mmtt) REVERT: C 232 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7562 (mm-30) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.2031 time to fit residues: 38.0300 Evaluate side-chains 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.0670 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 126 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148668 restraints weight = 24319.934| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.80 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2189 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= 0.119 Angle : 0.645 20.366 15018 Z= 0.315 Chirality : 0.045 0.394 1821 Planarity : 0.005 0.084 1866 Dihedral : 6.658 58.240 1602 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.95 % Allowed : 7.98 % Favored : 91.07 % 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: -0.77 (0.23), residues: 1377 helix: 1.44 (0.27), residues: 438 sheet: -0.00 (0.26), residues: 363 loop : -2.50 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.002 0.001 HIS A 317 PHE 0.006 0.001 PHE C 137 TYR 0.010 0.001 TYR C 299 ARG 0.003 0.000 ARG B 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01320 ( 6) link_NAG-ASN : angle 9.72879 ( 18) hydrogen bonds : bond 0.03812 ( 468) hydrogen bonds : angle 4.21982 ( 1269) SS BOND : bond 0.00240 ( 21) SS BOND : angle 1.15603 ( 42) covalent geometry : bond 0.00268 (11028) covalent geometry : angle 0.54725 (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 134 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.297 Fit side-chains REVERT: A 198 TYR cc_start: 0.8448 (t80) cc_final: 0.8146 (t80) REVERT: A 235 ARG cc_start: 0.6565 (ttm170) cc_final: 0.6264 (mmt180) REVERT: A 363 ASN cc_start: 0.8185 (p0) cc_final: 0.7911 (p0) REVERT: A 370 MET cc_start: 0.8568 (ttp) cc_final: 0.8258 (ttp) REVERT: A 427 LYS cc_start: 0.6661 (pttt) cc_final: 0.6373 (mptt) REVERT: B 235 ARG cc_start: 0.6338 (ttm170) cc_final: 0.5926 (mmt180) REVERT: B 427 LYS cc_start: 0.6472 (pttt) cc_final: 0.6182 (mmtt) REVERT: C 235 ARG cc_start: 0.6441 (ttm170) cc_final: 0.6027 (mmt180) REVERT: C 363 ASN cc_start: 0.8162 (p0) cc_final: 0.7879 (p0) outliers start: 12 outliers final: 11 residues processed: 130 average time/residue: 0.2322 time to fit residues: 43.5890 Evaluate side-chains 129 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 144 VAL 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: 0.9980 chunk 100 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.174528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145104 restraints weight = 22875.672| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.63 r_work: 0.3446 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11055 Z= 0.154 Angle : 0.661 18.114 15018 Z= 0.328 Chirality : 0.047 0.449 1821 Planarity : 0.005 0.087 1866 Dihedral : 6.300 52.738 1602 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.18 % Allowed : 8.77 % Favored : 90.05 % 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: -0.87 (0.22), residues: 1377 helix: 1.30 (0.27), residues: 438 sheet: -0.05 (0.25), residues: 363 loop : -2.52 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 314 HIS 0.001 0.001 HIS C 317 PHE 0.009 0.001 PHE C 137 TYR 0.014 0.001 TYR B 441 ARG 0.003 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01275 ( 6) link_NAG-ASN : angle 8.69784 ( 18) hydrogen bonds : bond 0.04578 ( 468) hydrogen bonds : angle 4.32724 ( 1269) SS BOND : bond 0.00317 ( 21) SS BOND : angle 1.41713 ( 42) covalent geometry : bond 0.00379 (11028) covalent geometry : angle 0.58491 (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 132 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.136 Fit side-chains REVERT: A 198 TYR cc_start: 0.8370 (t80) cc_final: 0.7978 (t80) REVERT: A 235 ARG cc_start: 0.7245 (ttm170) cc_final: 0.6207 (mmt180) REVERT: A 370 MET cc_start: 0.8626 (ttp) cc_final: 0.8353 (ttp) REVERT: A 427 LYS cc_start: 0.7042 (pttt) cc_final: 0.6495 (mptt) REVERT: B 427 LYS cc_start: 0.6846 (pttt) cc_final: 0.6290 (mmtt) REVERT: C 92 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7739 (tt0) REVERT: C 309 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7989 (mm) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.2084 time to fit residues: 38.7824 Evaluate side-chains 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain 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 377 SER Chi-restraints excluded: chain B residue 384 VAL 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 Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.0270 chunk 133 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.176505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147973 restraints weight = 25149.478| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.27 r_work: 0.3416 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11055 Z= 0.125 Angle : 0.611 16.852 15018 Z= 0.306 Chirality : 0.046 0.468 1821 Planarity : 0.005 0.081 1866 Dihedral : 6.172 53.251 1602 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.79 % Allowed : 9.48 % Favored : 89.73 % 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: -0.74 (0.23), residues: 1377 helix: 1.41 (0.27), residues: 438 sheet: 0.04 (0.25), residues: 363 loop : -2.46 (0.23), residues: 576 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 0.007 0.001 PHE C 137 TYR 0.011 0.001 TYR C 299 ARG 0.002 0.000 ARG A 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01350 ( 6) link_NAG-ASN : angle 7.93156 ( 18) hydrogen bonds : bond 0.03894 ( 468) hydrogen bonds : angle 4.15710 ( 1269) SS BOND : bond 0.00267 ( 21) SS BOND : angle 1.16212 ( 42) covalent geometry : bond 0.00295 (11028) covalent geometry : angle 0.54384 (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 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.098 Fit side-chains REVERT: A 198 TYR cc_start: 0.8360 (t80) cc_final: 0.8011 (t80) REVERT: A 235 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6225 (mmt180) REVERT: A 370 MET cc_start: 0.8615 (ttp) cc_final: 0.8325 (ttp) REVERT: A 427 LYS cc_start: 0.7092 (pttt) cc_final: 0.6512 (mptt) REVERT: B 235 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6006 (mmt180) REVERT: B 427 LYS cc_start: 0.6796 (pttt) cc_final: 0.6231 (mmtt) REVERT: C 92 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7853 (tt0) REVERT: C 235 ARG cc_start: 0.7177 (ttm170) cc_final: 0.6080 (mmt180) REVERT: C 309 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7949 (mm) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.2270 time to fit residues: 38.4957 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 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 Chi-restraints excluded: chain C residue 309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.0010 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.3904 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.179192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150671 restraints weight = 22743.970| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.73 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11055 Z= 0.106 Angle : 0.572 15.589 15018 Z= 0.288 Chirality : 0.046 0.456 1821 Planarity : 0.004 0.078 1866 Dihedral : 5.609 53.195 1596 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.32 % Allowed : 10.11 % 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: -0.51 (0.23), residues: 1377 helix: 1.63 (0.27), residues: 438 sheet: 0.23 (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 C 317 PHE 0.005 0.001 PHE B 351 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 0.01304 ( 6) link_NAG-ASN : angle 7.25893 ( 18) hydrogen bonds : bond 0.03152 ( 468) hydrogen bonds : angle 3.93202 ( 1269) SS BOND : bond 0.00212 ( 21) SS BOND : angle 0.97137 ( 42) covalent geometry : bond 0.00236 (11028) covalent geometry : angle 0.51208 (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 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 1.221 Fit side-chains REVERT: A 198 TYR cc_start: 0.8353 (t80) cc_final: 0.8152 (t80) REVERT: A 235 ARG cc_start: 0.6571 (ttm170) cc_final: 0.6076 (mmt180) REVERT: A 370 MET cc_start: 0.8523 (ttp) cc_final: 0.8254 (ttp) REVERT: A 417 TYR cc_start: 0.8434 (m-80) cc_final: 0.8190 (m-80) REVERT: A 427 LYS cc_start: 0.6767 (pttt) cc_final: 0.6434 (mptt) REVERT: B 235 ARG cc_start: 0.6325 (ttm170) cc_final: 0.5804 (mmt180) REVERT: B 427 LYS cc_start: 0.6489 (pttt) cc_final: 0.6157 (mmtt) REVERT: C 235 ARG cc_start: 0.6493 (ttm170) cc_final: 0.5920 (mmt180) outliers start: 4 outliers final: 3 residues processed: 124 average time/residue: 0.2206 time to fit residues: 39.6478 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER 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: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 0.0670 chunk 98 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0520 ------------------------------------------------------------------------------- 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 371 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 = 0.3990 r_free = 0.3990 target = 0.172129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143880 restraints weight = 29081.017| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.69 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11055 Z= 0.153 Angle : 0.619 14.973 15018 Z= 0.314 Chirality : 0.048 0.468 1821 Planarity : 0.005 0.085 1866 Dihedral : 5.706 50.725 1596 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.63 % Allowed : 10.19 % Favored : 89.18 % 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: -0.65 (0.23), residues: 1377 helix: 1.48 (0.26), residues: 438 sheet: 0.09 (0.25), residues: 363 loop : -2.40 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 314 HIS 0.001 0.001 HIS C 317 PHE 0.009 0.001 PHE C 137 TYR 0.014 0.001 TYR B 441 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01250 ( 6) link_NAG-ASN : angle 6.93042 ( 18) hydrogen bonds : bond 0.04320 ( 468) hydrogen bonds : angle 4.18299 ( 1269) SS BOND : bond 0.00297 ( 21) SS BOND : angle 1.21250 ( 42) covalent geometry : bond 0.00379 (11028) covalent geometry : angle 0.56816 (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: 8 poor density : 112 time to evaluate : 1.224 Fit side-chains REVERT: A 198 TYR cc_start: 0.8450 (t80) cc_final: 0.8206 (t80) REVERT: A 235 ARG cc_start: 0.6638 (ttm170) cc_final: 0.6366 (mmt180) REVERT: A 370 MET cc_start: 0.8575 (ttp) cc_final: 0.8278 (ttp) REVERT: A 427 LYS cc_start: 0.6718 (pttt) cc_final: 0.6503 (mptt) REVERT: B 235 ARG cc_start: 0.6527 (ttm170) cc_final: 0.6133 (mmt180) REVERT: C 235 ARG cc_start: 0.6615 (ttm170) cc_final: 0.6369 (mmt180) outliers start: 8 outliers final: 7 residues processed: 115 average time/residue: 0.2455 time to fit residues: 40.4822 Evaluate side-chains 117 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain B residue 144 VAL 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: 0.8980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 9 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.176827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149154 restraints weight = 21670.194| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.42 r_work: 0.3441 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11055 Z= 0.122 Angle : 0.579 13.959 15018 Z= 0.296 Chirality : 0.047 0.463 1821 Planarity : 0.005 0.078 1866 Dihedral : 5.673 51.692 1596 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.71 % Allowed : 10.11 % Favored : 89.18 % 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: -0.54 (0.23), residues: 1377 helix: 1.56 (0.27), residues: 438 sheet: 0.20 (0.25), residues: 360 loop : -2.36 (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 C 317 PHE 0.007 0.001 PHE C 137 TYR 0.011 0.001 TYR B 299 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01241 ( 6) link_NAG-ASN : angle 6.46380 ( 18) hydrogen bonds : bond 0.03757 ( 468) hydrogen bonds : angle 4.05312 ( 1269) SS BOND : bond 0.00271 ( 21) SS BOND : angle 1.02493 ( 42) covalent geometry : bond 0.00288 (11028) covalent geometry : angle 0.53241 (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 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.142 Fit side-chains REVERT: A 92 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7710 (tt0) REVERT: A 198 TYR cc_start: 0.8357 (t80) cc_final: 0.8070 (t80) REVERT: A 235 ARG cc_start: 0.7262 (ttm170) cc_final: 0.6231 (mmt180) REVERT: A 370 MET cc_start: 0.8594 (ttp) cc_final: 0.8330 (ttp) REVERT: A 427 LYS cc_start: 0.7240 (pttt) cc_final: 0.6756 (mptt) REVERT: B 235 ARG cc_start: 0.7139 (ttm170) cc_final: 0.6004 (mmt180) REVERT: B 427 LYS cc_start: 0.6796 (pttt) cc_final: 0.6200 (mmtt) REVERT: C 235 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6186 (mmt180) outliers start: 9 outliers final: 9 residues processed: 114 average time/residue: 0.2269 time to fit residues: 37.1128 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 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 B residue 384 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 0.3980 chunk 128 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 overall best weight: 0.3584 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.179618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150969 restraints weight = 23767.066| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.74 r_work: 0.3451 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11055 Z= 0.103 Angle : 0.542 12.704 15018 Z= 0.278 Chirality : 0.046 0.439 1821 Planarity : 0.004 0.079 1866 Dihedral : 5.508 52.554 1596 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.47 % Allowed : 10.35 % Favored : 89.18 % 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: -0.36 (0.23), residues: 1377 helix: 1.70 (0.27), residues: 441 sheet: 0.28 (0.25), residues: 357 loop : -2.23 (0.24), 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 0.005 0.001 PHE B 351 TYR 0.010 0.001 TYR B 299 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 6) link_NAG-ASN : angle 5.87648 ( 18) hydrogen bonds : bond 0.03015 ( 468) hydrogen bonds : angle 3.84785 ( 1269) SS BOND : bond 0.00221 ( 21) SS BOND : angle 0.85508 ( 42) covalent geometry : bond 0.00228 (11028) covalent geometry : angle 0.50173 (14958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4658.73 seconds wall clock time: 81 minutes 45.23 seconds (4905.23 seconds total)