Starting phenix.real_space_refine on Wed Sep 17 19:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2x_44117/09_2025/9b2x_44117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2x_44117/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b2x_44117/09_2025/9b2x_44117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2x_44117/09_2025/9b2x_44117_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2x_44117/09_2025/9b2x_44117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2x_44117/09_2025/9b2x_44117.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C Time building chain proxies: 3.20, per 1000 atoms: 0.29 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 B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 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: 1.04 Conformation dependent library (CDL) restraints added in 873.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.44 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: 1.69 Time building geometry restraints manager: 1.37 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 12.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- 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 : 3.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG A 507 TYR 0.013 0.001 TYR A 441 PHE 0.015 0.001 PHE B 237 TRP 0.008 0.001 TRP A 52 HIS 0.002 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00285 (11028) covalent geometry : angle 0.57925 (14958) SS BOND : bond 0.00169 ( 21) SS BOND : angle 0.89170 ( 42) hydrogen bonds : bond 0.21287 ( 468) hydrogen bonds : angle 6.72208 ( 1269) link_NAG-ASN : bond 0.01370 ( 6) link_NAG-ASN : angle 8.24040 ( 18) *********************** 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 : 0.363 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: 0.0999 time to fit residues: 22.1305 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 : 0.388 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3713 r_free = 0.3713 target = 0.150905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116725 restraints weight = 29584.371| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.43 r_work: 0.3078 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11055 Z= 0.154 Angle : 0.696 15.528 15018 Z= 0.348 Chirality : 0.050 0.494 1821 Planarity : 0.005 0.091 1866 Dihedral : 8.678 49.447 1602 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.95 % Allowed : 5.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.23), residues: 1377 helix: 1.34 (0.27), residues: 438 sheet: -0.13 (0.26), residues: 360 loop : -2.56 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 507 TYR 0.014 0.001 TYR C 299 PHE 0.009 0.001 PHE C 137 TRP 0.010 0.002 TRP A 314 HIS 0.002 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00367 (11028) covalent geometry : angle 0.64526 (14958) SS BOND : bond 0.00297 ( 21) SS BOND : angle 1.57241 ( 42) hydrogen bonds : bond 0.04713 ( 468) hydrogen bonds : angle 4.78490 ( 1269) link_NAG-ASN : bond 0.01242 ( 6) link_NAG-ASN : angle 7.20724 ( 18) *********************** 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 123 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.396 Fit side-chains REVERT: A 232 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 370 MET cc_start: 0.8297 (ttp) cc_final: 0.8084 (ttp) REVERT: A 427 LYS cc_start: 0.6778 (pttt) cc_final: 0.6226 (mmtt) REVERT: B 161 GLU cc_start: 0.7758 (pp20) cc_final: 0.7482 (mm-30) REVERT: B 227 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7301 (m110) REVERT: B 232 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 294 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7275 (tt0) REVERT: C 232 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7319 (mm-30) REVERT: C 427 LYS cc_start: 0.6755 (pttt) cc_final: 0.6190 (mmtt) REVERT: C 509 PHE cc_start: 0.6259 (t80) cc_final: 0.6034 (t80) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.0848 time to fit residues: 15.0154 Evaluate side-chains 115 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 B residue 144 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 227 ASN 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 4 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.172353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143267 restraints weight = 20372.908| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.57 r_work: 0.3412 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11055 Z= 0.199 Angle : 0.702 14.363 15018 Z= 0.358 Chirality : 0.051 0.478 1821 Planarity : 0.005 0.094 1866 Dihedral : 6.916 52.531 1602 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.03 % Allowed : 6.95 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.22), residues: 1377 helix: 1.06 (0.26), residues: 438 sheet: -0.12 (0.25), residues: 360 loop : -2.61 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 507 TYR 0.018 0.002 TYR B 441 PHE 0.012 0.002 PHE C 137 TRP 0.011 0.002 TRP A 52 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00500 (11028) covalent geometry : angle 0.65751 (14958) SS BOND : bond 0.00362 ( 21) SS BOND : angle 1.75840 ( 42) hydrogen bonds : bond 0.05801 ( 468) hydrogen bonds : angle 4.78277 ( 1269) link_NAG-ASN : bond 0.01055 ( 6) link_NAG-ASN : angle 6.72372 ( 18) *********************** 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 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 370 MET cc_start: 0.8651 (ttp) cc_final: 0.8385 (ttp) REVERT: A 427 LYS cc_start: 0.7045 (pttt) cc_final: 0.6512 (mptt) REVERT: B 232 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 427 LYS cc_start: 0.6777 (pttt) cc_final: 0.6248 (mmtt) REVERT: C 232 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7544 (mm-30) outliers start: 13 outliers final: 11 residues processed: 120 average time/residue: 0.0851 time to fit residues: 15.2830 Evaluate side-chains 120 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 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 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 292 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** 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 = 0.3986 r_free = 0.3986 target = 0.172310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142489 restraints weight = 19714.831| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.58 r_work: 0.3400 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11055 Z= 0.192 Angle : 0.711 20.450 15018 Z= 0.355 Chirality : 0.048 0.464 1821 Planarity : 0.005 0.091 1866 Dihedral : 6.883 55.010 1602 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.74 % Allowed : 7.58 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.22), residues: 1377 helix: 1.08 (0.26), residues: 438 sheet: -0.21 (0.25), residues: 363 loop : -2.63 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 507 TYR 0.016 0.002 TYR B 441 PHE 0.012 0.002 PHE C 137 TRP 0.011 0.002 TRP A 52 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00484 (11028) covalent geometry : angle 0.63776 (14958) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.55835 ( 42) hydrogen bonds : bond 0.05415 ( 468) hydrogen bonds : angle 4.61137 ( 1269) link_NAG-ASN : bond 0.01197 ( 6) link_NAG-ASN : angle 8.82931 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 207 VAL cc_start: 0.5490 (OUTLIER) cc_final: 0.5249 (m) REVERT: A 370 MET cc_start: 0.8636 (ttp) cc_final: 0.8309 (ttp) REVERT: A 427 LYS cc_start: 0.7035 (pttt) cc_final: 0.6469 (mptt) REVERT: B 232 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 427 LYS cc_start: 0.6836 (pttt) cc_final: 0.6261 (mmtt) REVERT: C 232 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7602 (mm-30) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.0969 time to fit residues: 18.3118 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 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 57 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 428 ASN B 380 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.174501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145841 restraints weight = 23375.417| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.77 r_work: 0.3395 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2225 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= 0.151 Angle : 0.651 17.863 15018 Z= 0.328 Chirality : 0.047 0.438 1821 Planarity : 0.005 0.090 1866 Dihedral : 6.533 52.241 1602 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.42 % Allowed : 8.06 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.22), residues: 1377 helix: 1.20 (0.27), residues: 438 sheet: -0.12 (0.25), residues: 363 loop : -2.60 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 507 TYR 0.013 0.001 TYR C 441 PHE 0.009 0.001 PHE C 137 TRP 0.010 0.002 TRP A 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00369 (11028) covalent geometry : angle 0.58957 (14958) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.42552 ( 42) hydrogen bonds : bond 0.04644 ( 468) hydrogen bonds : angle 4.41902 ( 1269) link_NAG-ASN : bond 0.01124 ( 6) link_NAG-ASN : angle 7.73712 ( 18) *********************** 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 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 207 VAL cc_start: 0.5427 (OUTLIER) cc_final: 0.5152 (m) REVERT: A 235 ARG cc_start: 0.7316 (ttm170) cc_final: 0.6241 (mmt180) REVERT: A 370 MET cc_start: 0.8622 (ttp) cc_final: 0.8338 (ttp) REVERT: A 427 LYS cc_start: 0.6997 (pttt) cc_final: 0.6437 (mmtt) REVERT: B 232 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 427 LYS cc_start: 0.6781 (pttt) cc_final: 0.6238 (mmtt) REVERT: C 232 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7703 (mm-30) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.1030 time to fit residues: 18.6088 Evaluate side-chains 127 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 451 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 425 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 380 ASN A 428 ASN B 380 ASN B 428 ASN C 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144253 restraints weight = 26381.560| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.66 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11055 Z= 0.172 Angle : 0.662 16.597 15018 Z= 0.337 Chirality : 0.048 0.458 1821 Planarity : 0.005 0.089 1866 Dihedral : 6.398 50.500 1602 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 1.82 % Allowed : 8.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.22), residues: 1377 helix: 1.09 (0.26), residues: 438 sheet: -0.15 (0.25), residues: 363 loop : -2.62 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 507 TYR 0.015 0.002 TYR B 441 PHE 0.011 0.001 PHE C 137 TRP 0.010 0.002 TRP A 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00429 (11028) covalent geometry : angle 0.61133 (14958) SS BOND : bond 0.00330 ( 21) SS BOND : angle 1.58318 ( 42) hydrogen bonds : bond 0.05060 ( 468) hydrogen bonds : angle 4.47436 ( 1269) link_NAG-ASN : bond 0.01084 ( 6) link_NAG-ASN : angle 7.04758 ( 18) *********************** 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 137 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.440 Fit side-chains REVERT: A 235 ARG cc_start: 0.6631 (ttm170) cc_final: 0.6315 (mmt180) REVERT: A 370 MET cc_start: 0.8615 (ttp) cc_final: 0.8326 (ttp) REVERT: A 427 LYS cc_start: 0.6740 (pttt) cc_final: 0.6422 (mmtt) REVERT: B 232 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 427 LYS cc_start: 0.6413 (pttt) cc_final: 0.6068 (mmtt) REVERT: C 232 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7091 (mm-30) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.0982 time to fit residues: 18.9262 Evaluate side-chains 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 384 VAL 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 Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 32 optimal weight: 0.2980 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 428 ASN B 227 ASN B 428 ASN C 380 ASN C 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149836 restraints weight = 22775.451| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.54 r_work: 0.3445 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2381 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= 0.112 Angle : 0.613 21.061 15018 Z= 0.304 Chirality : 0.046 0.463 1821 Planarity : 0.005 0.083 1866 Dihedral : 6.623 59.429 1602 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.47 % Allowed : 9.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.23), residues: 1377 helix: 1.48 (0.27), residues: 438 sheet: 0.10 (0.25), residues: 360 loop : -2.51 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 507 TYR 0.010 0.001 TYR A 299 PHE 0.015 0.001 PHE B 509 TRP 0.011 0.001 TRP A 314 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00248 (11028) covalent geometry : angle 0.53578 (14958) SS BOND : bond 0.00224 ( 21) SS BOND : angle 1.02701 ( 42) hydrogen bonds : bond 0.03527 ( 468) hydrogen bonds : angle 4.11297 ( 1269) link_NAG-ASN : bond 0.01437 ( 6) link_NAG-ASN : angle 8.49586 ( 18) *********************** 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 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.446 Fit side-chains REVERT: A 198 TYR cc_start: 0.8372 (t80) cc_final: 0.8030 (t80) REVERT: A 235 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6151 (mmt180) REVERT: A 370 MET cc_start: 0.8588 (ttp) cc_final: 0.8330 (ttp) REVERT: A 427 LYS cc_start: 0.6994 (pttt) cc_final: 0.6425 (mptt) REVERT: B 232 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 235 ARG cc_start: 0.7143 (ttm170) cc_final: 0.5947 (mmt180) REVERT: C 232 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7713 (mm-30) REVERT: C 235 ARG cc_start: 0.7200 (ttm170) cc_final: 0.5968 (mmt180) REVERT: C 427 LYS cc_start: 0.6836 (pttt) cc_final: 0.6393 (mmtt) outliers start: 6 outliers final: 5 residues processed: 126 average time/residue: 0.1148 time to fit residues: 20.6453 Evaluate side-chains 121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 124 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3966 r_free = 0.3966 target = 0.169579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141549 restraints weight = 26131.519| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.31 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11055 Z= 0.187 Angle : 0.682 19.772 15018 Z= 0.343 Chirality : 0.048 0.475 1821 Planarity : 0.005 0.092 1866 Dihedral : 6.262 54.473 1600 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.03 % Allowed : 10.11 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.22), residues: 1377 helix: 1.18 (0.26), residues: 438 sheet: -0.05 (0.25), residues: 363 loop : -2.60 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 507 TYR 0.016 0.002 TYR B 441 PHE 0.017 0.002 PHE B 509 TRP 0.009 0.002 TRP A 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00470 (11028) covalent geometry : angle 0.61931 (14958) SS BOND : bond 0.00357 ( 21) SS BOND : angle 1.38796 ( 42) hydrogen bonds : bond 0.05147 ( 468) hydrogen bonds : angle 4.44342 ( 1269) link_NAG-ASN : bond 0.01198 ( 6) link_NAG-ASN : angle 8.04349 ( 18) *********************** 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 128 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.557 Fit side-chains REVERT: A 235 ARG cc_start: 0.6662 (ttm170) cc_final: 0.6390 (mmt180) REVERT: A 370 MET cc_start: 0.8618 (ttp) cc_final: 0.8325 (ttp) REVERT: A 427 LYS cc_start: 0.6761 (pttt) cc_final: 0.6495 (mmtt) REVERT: B 232 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 427 LYS cc_start: 0.6512 (pttt) cc_final: 0.6115 (mmtt) outliers start: 13 outliers final: 12 residues processed: 124 average time/residue: 0.1045 time to fit residues: 19.1869 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 12 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 227 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 = 0.3987 r_free = 0.3987 target = 0.171800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144019 restraints weight = 20143.406| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.56 r_work: 0.3474 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11055 Z= 0.139 Angle : 0.620 18.553 15018 Z= 0.314 Chirality : 0.047 0.468 1821 Planarity : 0.005 0.085 1866 Dihedral : 6.168 55.769 1600 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.79 % Allowed : 10.51 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.22), residues: 1377 helix: 1.33 (0.26), residues: 438 sheet: 0.00 (0.25), residues: 363 loop : -2.55 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 507 TYR 0.011 0.001 TYR C 441 PHE 0.017 0.001 PHE B 509 TRP 0.010 0.002 TRP C 314 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00334 (11028) covalent geometry : angle 0.56199 (14958) SS BOND : bond 0.00305 ( 21) SS BOND : angle 1.14237 ( 42) hydrogen bonds : bond 0.04256 ( 468) hydrogen bonds : angle 4.22988 ( 1269) link_NAG-ASN : bond 0.01243 ( 6) link_NAG-ASN : angle 7.41447 ( 18) *********************** 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 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.451 Fit side-chains REVERT: A 198 TYR cc_start: 0.8405 (t80) cc_final: 0.8039 (t80) REVERT: A 235 ARG cc_start: 0.7245 (ttm170) cc_final: 0.6270 (mmt180) REVERT: A 370 MET cc_start: 0.8626 (ttp) cc_final: 0.8351 (ttp) REVERT: A 427 LYS cc_start: 0.7048 (pttt) cc_final: 0.6532 (mmtt) REVERT: B 232 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 235 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6136 (mmt180) REVERT: B 427 LYS cc_start: 0.6755 (pttt) cc_final: 0.6206 (mmtt) REVERT: C 235 ARG cc_start: 0.7045 (ttm170) cc_final: 0.6030 (mmt180) REVERT: C 427 LYS cc_start: 0.6860 (pttt) cc_final: 0.6463 (mmtt) outliers start: 10 outliers final: 9 residues processed: 120 average time/residue: 0.1143 time to fit residues: 19.6218 Evaluate side-chains 124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 169 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 104 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 134 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.176890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149347 restraints weight = 15956.899| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.42 r_work: 0.3477 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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= 0.117 Angle : 0.582 17.473 15018 Z= 0.296 Chirality : 0.046 0.443 1821 Planarity : 0.005 0.085 1866 Dihedral : 5.835 54.602 1598 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.63 % Allowed : 10.58 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.23), residues: 1377 helix: 1.55 (0.27), residues: 435 sheet: 0.15 (0.25), residues: 360 loop : -2.52 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 507 TYR 0.010 0.001 TYR C 299 PHE 0.014 0.001 PHE B 509 TRP 0.011 0.001 TRP C 314 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00269 (11028) covalent geometry : angle 0.53007 (14958) SS BOND : bond 0.00270 ( 21) SS BOND : angle 0.98406 ( 42) hydrogen bonds : bond 0.03547 ( 468) hydrogen bonds : angle 4.03686 ( 1269) link_NAG-ASN : bond 0.01230 ( 6) link_NAG-ASN : angle 6.81173 ( 18) ********************** 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 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.477 Fit side-chains REVERT: A 198 TYR cc_start: 0.8372 (t80) cc_final: 0.8061 (t80) REVERT: A 235 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6137 (mmt180) REVERT: A 370 MET cc_start: 0.8599 (ttp) cc_final: 0.8348 (ttp) REVERT: A 417 TYR cc_start: 0.8491 (m-80) cc_final: 0.8288 (m-80) REVERT: A 427 LYS cc_start: 0.6992 (pttt) cc_final: 0.6493 (mptt) REVERT: B 232 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 235 ARG cc_start: 0.7073 (ttm170) cc_final: 0.5929 (mmt180) REVERT: C 235 ARG cc_start: 0.7092 (ttm170) cc_final: 0.5962 (mmt180) outliers start: 8 outliers final: 8 residues processed: 117 average time/residue: 0.1131 time to fit residues: 18.9070 Evaluate side-chains 122 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 169 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 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 134 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.169114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139184 restraints weight = 22487.506| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.69 r_work: 0.3410 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 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 = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11055 Z= 0.126 Angle : 0.586 16.692 15018 Z= 0.299 Chirality : 0.046 0.434 1821 Planarity : 0.005 0.082 1866 Dihedral : 5.673 53.545 1596 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.71 % Allowed : 10.51 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1377 helix: 1.62 (0.27), residues: 432 sheet: 0.14 (0.25), residues: 360 loop : -2.49 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 507 TYR 0.011 0.001 TYR C 441 PHE 0.015 0.001 PHE B 509 TRP 0.010 0.001 TRP A 314 HIS 0.001 0.000 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00300 (11028) covalent geometry : angle 0.54088 (14958) SS BOND : bond 0.00279 ( 21) SS BOND : angle 1.06735 ( 42) hydrogen bonds : bond 0.03876 ( 468) hydrogen bonds : angle 4.09784 ( 1269) link_NAG-ASN : bond 0.01173 ( 6) link_NAG-ASN : angle 6.41862 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.78 seconds wall clock time: 42 minutes 39.26 seconds (2559.26 seconds total)