Starting phenix.real_space_refine on Thu Jul 2 21:55:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmx_29299/07_2026/8fmx_29299.cif" } resolution = 3.37 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= 0.017 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 54 5.16 5 C 6504 2.51 5 N 1713 2.21 5 O 2058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10329 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3390 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.21 Number of scatterers: 10329 At special positions: 0 Unit cell: (109.375, 106.094, 112.656, 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 54 16.00 O 2058 8.00 N 1713 7.00 C 6504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 501 " - " ASN A 65 " " NAG B 501 " - " ASN B 65 " " NAG C 501 " - " ASN C 65 " " NAG D 1 " - " ASN A 459 " " NAG E 1 " - " ASN B 459 " " NAG F 1 " - " ASN C 459 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 288.7 milliseconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 40.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.667A pdb=" N LEU A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.649A pdb=" N GLU A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.758A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.662A pdb=" N ILE A 182 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.523A pdb=" N LEU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 353 No H-bonds generated for 'chain 'A' and resid 352 through 353' Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.648A pdb=" N LYS A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.242A pdb=" N THR A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.629A pdb=" N LEU B 28 " --> pdb=" O HIS B 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.654A pdb=" N GLU B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 179 through 182 removed outlier: 3.554A pdb=" N ILE B 182 " --> pdb=" O ILE B 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 186 through 215 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.546A pdb=" N LEU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.661A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.553A pdb=" N CYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 353 No H-bonds generated for 'chain 'B' and resid 352 through 353' Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N LYS B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 358 " --> pdb=" O THR B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 358' Processing helix chain 'B' and resid 447 through 465 removed outlier: 3.616A pdb=" N GLY B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.640A pdb=" N LEU C 28 " --> pdb=" O HIS C 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 94 removed outlier: 3.600A pdb=" N GLU C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 179 through 182 removed outlier: 3.588A pdb=" N ILE C 182 " --> pdb=" O ILE C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 186 through 215 Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.537A pdb=" N LEU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 removed outlier: 3.663A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 352 through 353 No H-bonds generated for 'chain 'C' and resid 352 through 353' Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N LYS C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS C 358 " --> pdb=" O THR C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 358' Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.676A pdb=" N GLY C 452 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157 removed outlier: 8.081A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 279 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 277 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 49 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 275 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 51 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 273 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 53 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 271 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222 removed outlier: 6.795A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 271 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 53 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 273 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 51 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 275 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 49 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 277 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 279 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 41 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ASN A 285 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N TYR A 39 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N VAL A 287 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N LEU A 37 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN A 289 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 35 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A 291 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 33 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.548A pdb=" N ALA A 108 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER C 423 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 110 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.901A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 407 removed outlier: 3.903A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.940A pdb=" N LEU A 421 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 157 removed outlier: 7.948A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 279 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 277 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 49 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 275 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 51 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 273 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 53 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 271 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.810A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 271 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 53 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 273 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 51 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 275 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 49 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 277 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 279 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 41 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ASN B 285 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N TYR B 39 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL B 287 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N LEU B 37 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N GLN B 289 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LYS B 35 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 291 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 33 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.904A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.923A pdb=" N LEU B 421 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 157 removed outlier: 7.952A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN C 279 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE C 277 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 49 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 275 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 51 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU C 273 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 53 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 271 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.813A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 271 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL C 53 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU C 273 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 51 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 275 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR C 49 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE C 277 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN C 279 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 41 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ASN C 285 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N TYR C 39 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N VAL C 287 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N LEU C 37 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN C 289 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N LYS C 35 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU C 291 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 33 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL C 333 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298 471 hydrogen bonds defined for protein. 1287 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: 1.41 Time building geometry restraints manager: 1.14 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: 3399 1.34 - 1.46: 1207 1.46 - 1.57: 5778 1.57 - 1.69: 2 1.69 - 1.81: 78 Bond restraints: 10464 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.600 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.467 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 12939 1.52 - 3.04: 1064 3.04 - 4.56: 192 4.56 - 6.08: 33 6.08 - 7.60: 7 Bond angle restraints: 14235 Sorted by residual: angle pdb=" N ILE C 446 " pdb=" CA ILE C 446 " pdb=" C ILE C 446 " ideal model delta sigma weight residual 107.75 112.97 -5.22 1.46e+00 4.69e-01 1.28e+01 angle pdb=" N ILE B 446 " pdb=" CA ILE B 446 " pdb=" C ILE B 446 " ideal model delta sigma weight residual 107.75 112.94 -5.19 1.46e+00 4.69e-01 1.26e+01 angle pdb=" N THR C 169 " pdb=" CA THR C 169 " pdb=" C THR C 169 " ideal model delta sigma weight residual 111.11 115.08 -3.97 1.20e+00 6.94e-01 1.09e+01 angle pdb=" N THR B 169 " pdb=" CA THR B 169 " pdb=" C THR B 169 " ideal model delta sigma weight residual 111.11 115.04 -3.93 1.20e+00 6.94e-01 1.07e+01 angle pdb=" N CYS C 66 " pdb=" CA CYS C 66 " pdb=" C CYS C 66 " ideal model delta sigma weight residual 113.41 117.27 -3.86 1.22e+00 6.72e-01 1.00e+01 ... (remaining 14230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5911 17.66 - 35.31: 323 35.31 - 52.97: 62 52.97 - 70.62: 24 70.62 - 88.27: 10 Dihedral angle restraints: 6330 sinusoidal: 2454 harmonic: 3876 Sorted by residual: dihedral pdb=" CA LYS A 161 " pdb=" C LYS A 161 " pdb=" N GLN A 162 " pdb=" CA GLN A 162 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -133.35 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ILE A 451 " pdb=" CA ILE A 451 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 6327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1486 0.072 - 0.143: 252 0.143 - 0.215: 28 0.215 - 0.286: 6 0.286 - 0.358: 4 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 459 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 459 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 459 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1773 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 206 " -0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C LEU C 206 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU C 206 " -0.029 2.00e-02 2.50e+03 pdb=" N THR C 207 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 459 " -0.027 2.00e-02 2.50e+03 2.63e-02 8.67e+00 pdb=" CG ASN A 459 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 459 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 459 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 296 " -0.008 2.00e-02 2.50e+03 1.91e-02 7.27e+00 pdb=" CG TYR B 296 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 296 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 296 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 296 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 296 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 296 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR B 296 " -0.029 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4103 2.90 - 3.40: 9866 3.40 - 3.90: 16690 3.90 - 4.40: 18183 4.40 - 4.90: 31375 Nonbonded interactions: 80217 Sorted by model distance: nonbonded pdb=" O THR A 315 " pdb=" OG1 THR A 316 " model vdw 2.404 3.040 nonbonded pdb=" O THR C 315 " pdb=" OG1 THR C 316 " model vdw 2.431 3.040 nonbonded pdb=" O THR B 315 " pdb=" OG1 THR B 316 " model vdw 2.436 3.040 nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.499 3.040 nonbonded pdb=" N ASP A 436 " pdb=" OD1 ASP A 436 " model vdw 2.500 3.120 ... (remaining 80212 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.680 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10491 Z= 0.254 Angle : 0.979 11.682 14301 Z= 0.558 Chirality : 0.056 0.358 1776 Planarity : 0.006 0.059 1812 Dihedral : 12.339 88.275 3795 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1329 helix: -0.60 (0.22), residues: 453 sheet: -0.18 (0.32), residues: 261 loop : -0.89 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 309 TYR 0.030 0.006 TYR B 201 PHE 0.023 0.003 PHE C 234 TRP 0.013 0.002 TRP B 303 HIS 0.005 0.002 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.25 (10464) covalent geometry : angle 0.93047 / 0.55 (14235) SS BOND : bond 0.00366 / 0.20 ( 15) SS BOND : angle 1.20388 / 0.85 ( 30) hydrogen bonds : bond 0.14068 / 9.27 ( 459) hydrogen bonds : angle 6.69389 / 4.76 ( 1287) link_BETA1-4 : bond 0.01768 / 0.88 ( 6) link_BETA1-4 : angle 5.29334 / 3.12 ( 18) link_NAG-ASN : bond 0.00841 / 0.44 ( 6) link_NAG-ASN : angle 6.82581 / 4.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.414 Fit side-chains REVERT: A 235 ASP cc_start: 0.8391 (t70) cc_final: 0.8179 (t70) REVERT: A 454 GLN cc_start: 0.8696 (mt0) cc_final: 0.8485 (mt0) REVERT: B 92 MET cc_start: 0.9215 (tpp) cc_final: 0.8997 (tpp) REVERT: C 92 MET cc_start: 0.9220 (tpp) cc_final: 0.8851 (tpp) REVERT: C 448 LYS cc_start: 0.9166 (mttt) cc_final: 0.8919 (tppp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1262 time to fit residues: 15.4506 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 ASN A 384 ASN A 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.035258 restraints weight = 44226.674| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.39 r_work: 0.2425 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10491 Z= 0.139 Angle : 0.648 9.735 14301 Z= 0.328 Chirality : 0.046 0.276 1776 Planarity : 0.004 0.052 1812 Dihedral : 4.948 20.615 1425 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.61 % Allowed : 4.34 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1329 helix: 1.06 (0.25), residues: 474 sheet: 0.39 (0.33), residues: 258 loop : -0.46 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 232 TYR 0.012 0.001 TYR A 41 PHE 0.017 0.002 PHE C 105 TRP 0.002 0.001 TRP C 303 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10464) covalent geometry : angle 0.61350 / 0.32 (14235) SS BOND : bond 0.00124 / 0.07 ( 15) SS BOND : angle 1.00621 / 0.68 ( 30) hydrogen bonds : bond 0.04431 / 3.03 ( 459) hydrogen bonds : angle 5.08241 / 3.56 ( 1287) link_BETA1-4 : bond 0.01409 / 0.70 ( 6) link_BETA1-4 : angle 3.13815 / 1.95 ( 18) link_NAG-ASN : bond 0.01548 / 0.77 ( 6) link_NAG-ASN : angle 4.97177 / 3.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 453 ASN cc_start: 0.9253 (m-40) cc_final: 0.8958 (m110) REVERT: A 454 GLN cc_start: 0.8968 (mt0) cc_final: 0.8663 (mp10) REVERT: B 92 MET cc_start: 0.9580 (tpp) cc_final: 0.9134 (tpp) REVERT: C 92 MET cc_start: 0.9643 (tpp) cc_final: 0.9165 (tpp) REVERT: C 110 MET cc_start: 0.9249 (tpp) cc_final: 0.9033 (tpt) REVERT: C 448 LYS cc_start: 0.9418 (mttt) cc_final: 0.8983 (tppp) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.0804 time to fit residues: 7.7748 Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 367 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 0.0370 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.046863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.035659 restraints weight = 44537.495| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 4.48 r_work: 0.2429 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10491 Z= 0.114 Angle : 0.567 8.977 14301 Z= 0.286 Chirality : 0.044 0.241 1776 Planarity : 0.003 0.036 1812 Dihedral : 4.593 17.581 1425 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.78 % Allowed : 5.30 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1329 helix: 1.66 (0.25), residues: 456 sheet: 0.40 (0.33), residues: 258 loop : -0.45 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.008 0.001 TYR A 41 PHE 0.011 0.001 PHE B 277 TRP 0.001 0.000 TRP C 303 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10464) covalent geometry : angle 0.53585 / 0.28 (14235) SS BOND : bond 0.00097 / 0.06 ( 15) SS BOND : angle 0.68802 / 0.50 ( 30) hydrogen bonds : bond 0.03771 / 2.58 ( 459) hydrogen bonds : angle 4.74638 / 3.32 ( 1287) link_BETA1-4 : bond 0.01297 / 0.64 ( 6) link_BETA1-4 : angle 2.95763 / 1.87 ( 18) link_NAG-ASN : bond 0.00896 / 0.45 ( 6) link_NAG-ASN : angle 4.29186 / 2.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.322 Fit side-chains REVERT: A 100 ASN cc_start: 0.9019 (t0) cc_final: 0.8578 (p0) REVERT: A 343 MET cc_start: 0.7664 (ptp) cc_final: 0.7059 (ptp) REVERT: A 453 ASN cc_start: 0.9380 (m-40) cc_final: 0.9024 (m110) REVERT: A 454 GLN cc_start: 0.8988 (mt0) cc_final: 0.8721 (mp10) REVERT: B 92 MET cc_start: 0.9600 (tpp) cc_final: 0.9205 (tpp) REVERT: C 92 MET cc_start: 0.9636 (tpp) cc_final: 0.9211 (tpp) REVERT: C 110 MET cc_start: 0.9109 (tpp) cc_final: 0.8846 (tpp) REVERT: C 292 MET cc_start: 0.9423 (mtm) cc_final: 0.9149 (mtm) REVERT: C 448 LYS cc_start: 0.9507 (mttt) cc_final: 0.9013 (tppp) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 0.0976 time to fit residues: 8.8045 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 127 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.037243 restraints weight = 45021.422| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 4.45 r_work: 0.2447 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10491 Z= 0.097 Angle : 0.534 8.691 14301 Z= 0.268 Chirality : 0.043 0.202 1776 Planarity : 0.003 0.034 1812 Dihedral : 4.345 15.809 1425 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.13 % Allowed : 5.47 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1329 helix: 1.81 (0.26), residues: 456 sheet: 0.30 (0.32), residues: 258 loop : -0.42 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.007 0.001 TYR C 415 PHE 0.009 0.001 PHE A 277 TRP 0.001 0.000 TRP C 303 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (10464) covalent geometry : angle 0.50624 / 0.26 (14235) SS BOND : bond 0.00079 / 0.05 ( 15) SS BOND : angle 0.57387 / 0.42 ( 30) hydrogen bonds : bond 0.03207 / 2.22 ( 459) hydrogen bonds : angle 4.52968 / 3.17 ( 1287) link_BETA1-4 : bond 0.01303 / 0.64 ( 6) link_BETA1-4 : angle 2.79187 / 1.76 ( 18) link_NAG-ASN : bond 0.00808 / 0.40 ( 6) link_NAG-ASN : angle 3.98476 / 2.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9516 (tpp) cc_final: 0.9203 (tpp) REVERT: A 110 MET cc_start: 0.9508 (tpt) cc_final: 0.9181 (tpt) REVERT: A 168 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: A 453 ASN cc_start: 0.9351 (m-40) cc_final: 0.9028 (m110) REVERT: A 454 GLN cc_start: 0.9017 (mt0) cc_final: 0.8718 (pt0) REVERT: B 92 MET cc_start: 0.9564 (tpp) cc_final: 0.9241 (tpp) REVERT: B 448 LYS cc_start: 0.9302 (mmtp) cc_final: 0.9079 (mmtp) REVERT: C 292 MET cc_start: 0.9435 (mtm) cc_final: 0.9155 (mtm) REVERT: C 448 LYS cc_start: 0.9513 (mttt) cc_final: 0.9023 (tppp) outliers start: 13 outliers final: 4 residues processed: 60 average time/residue: 0.0883 time to fit residues: 8.1982 Evaluate side-chains 49 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.046584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.035427 restraints weight = 45577.271| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 4.45 r_work: 0.2400 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10491 Z= 0.164 Angle : 0.569 9.757 14301 Z= 0.280 Chirality : 0.043 0.182 1776 Planarity : 0.003 0.033 1812 Dihedral : 4.331 16.064 1425 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.95 % Allowed : 5.90 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1329 helix: 1.93 (0.26), residues: 456 sheet: 0.27 (0.32), residues: 258 loop : -0.49 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.007 0.001 TYR C 249 PHE 0.011 0.001 PHE B 277 TRP 0.002 0.001 TRP B 303 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10464) covalent geometry : angle 0.54608 / 0.28 (14235) SS BOND : bond 0.00171 / 0.11 ( 15) SS BOND : angle 0.66994 / 0.50 ( 30) hydrogen bonds : bond 0.03484 / 2.39 ( 459) hydrogen bonds : angle 4.47575 / 3.16 ( 1287) link_BETA1-4 : bond 0.01164 / 0.57 ( 6) link_BETA1-4 : angle 2.67957 / 1.68 ( 18) link_NAG-ASN : bond 0.00642 / 0.32 ( 6) link_NAG-ASN : angle 3.61414 / 2.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9562 (tpp) cc_final: 0.9026 (tpp) REVERT: A 105 PHE cc_start: 0.8369 (t80) cc_final: 0.7984 (t80) REVERT: A 110 MET cc_start: 0.9544 (tpt) cc_final: 0.9208 (tpt) REVERT: A 241 MET cc_start: 0.9279 (mtm) cc_final: 0.9062 (mtm) REVERT: A 343 MET cc_start: 0.7851 (pmm) cc_final: 0.7360 (ptp) REVERT: A 453 ASN cc_start: 0.9375 (m-40) cc_final: 0.9058 (m110) REVERT: A 454 GLN cc_start: 0.8971 (mt0) cc_final: 0.8632 (mt0) REVERT: B 92 MET cc_start: 0.9605 (tpp) cc_final: 0.9251 (tpp) REVERT: C 92 MET cc_start: 0.9609 (tpp) cc_final: 0.9150 (tpp) REVERT: C 292 MET cc_start: 0.9455 (mtm) cc_final: 0.9183 (mtm) REVERT: C 299 ASP cc_start: 0.9048 (t0) cc_final: 0.8741 (t0) REVERT: C 448 LYS cc_start: 0.9498 (mttt) cc_final: 0.9042 (tppp) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 0.0842 time to fit residues: 7.4940 Evaluate side-chains 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.036024 restraints weight = 45833.398| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 4.38 r_work: 0.2405 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10491 Z= 0.155 Angle : 0.555 8.813 14301 Z= 0.276 Chirality : 0.043 0.200 1776 Planarity : 0.003 0.032 1812 Dihedral : 4.320 22.037 1425 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.52 % Allowed : 7.03 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1329 helix: 1.99 (0.25), residues: 456 sheet: 0.18 (0.32), residues: 261 loop : -0.45 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.007 0.001 TYR B 249 PHE 0.008 0.001 PHE B 277 TRP 0.002 0.000 TRP B 303 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10464) covalent geometry : angle 0.53406 / 0.27 (14235) SS BOND : bond 0.00157 / 0.10 ( 15) SS BOND : angle 0.69168 / 0.51 ( 30) hydrogen bonds : bond 0.03365 / 2.31 ( 459) hydrogen bonds : angle 4.37966 / 3.10 ( 1287) link_BETA1-4 : bond 0.01153 / 0.57 ( 6) link_BETA1-4 : angle 2.64229 / 1.67 ( 18) link_NAG-ASN : bond 0.00678 / 0.34 ( 6) link_NAG-ASN : angle 3.38508 / 2.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9559 (tpp) cc_final: 0.9033 (tpp) REVERT: A 105 PHE cc_start: 0.8436 (t80) cc_final: 0.8032 (t80) REVERT: A 110 MET cc_start: 0.9533 (tpt) cc_final: 0.9174 (tpt) REVERT: A 451 ILE cc_start: 0.9344 (tt) cc_final: 0.9026 (pt) REVERT: A 453 ASN cc_start: 0.9391 (m-40) cc_final: 0.9079 (m110) REVERT: A 454 GLN cc_start: 0.9058 (mt0) cc_final: 0.8635 (mt0) REVERT: B 92 MET cc_start: 0.9613 (tpp) cc_final: 0.9264 (tpp) REVERT: B 448 LYS cc_start: 0.9320 (mmtp) cc_final: 0.8915 (tppt) REVERT: C 292 MET cc_start: 0.9465 (mtm) cc_final: 0.9204 (mtm) REVERT: C 299 ASP cc_start: 0.9075 (t0) cc_final: 0.8758 (t0) REVERT: C 448 LYS cc_start: 0.9474 (mttt) cc_final: 0.8983 (tppp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.0891 time to fit residues: 7.3144 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.045068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.034047 restraints weight = 46058.428| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 4.42 r_work: 0.2380 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10491 Z= 0.199 Angle : 0.590 9.184 14301 Z= 0.290 Chirality : 0.043 0.183 1776 Planarity : 0.003 0.031 1812 Dihedral : 4.378 15.478 1425 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.61 % Allowed : 7.73 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1329 helix: 1.98 (0.25), residues: 456 sheet: 0.15 (0.32), residues: 261 loop : -0.48 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.008 0.001 TYR B 249 PHE 0.009 0.001 PHE B 277 TRP 0.002 0.000 TRP B 303 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (10464) covalent geometry : angle 0.57187 / 0.29 (14235) SS BOND : bond 0.00210 / 0.13 ( 15) SS BOND : angle 0.78443 / 0.57 ( 30) hydrogen bonds : bond 0.03558 / 2.44 ( 459) hydrogen bonds : angle 4.42118 / 3.12 ( 1287) link_BETA1-4 : bond 0.01098 / 0.54 ( 6) link_BETA1-4 : angle 2.64165 / 1.66 ( 18) link_NAG-ASN : bond 0.00595 / 0.30 ( 6) link_NAG-ASN : angle 3.10155 / 1.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9552 (tpp) cc_final: 0.9023 (tpp) REVERT: A 110 MET cc_start: 0.9529 (tpt) cc_final: 0.9135 (tpt) REVERT: A 453 ASN cc_start: 0.9398 (m-40) cc_final: 0.9118 (m110) REVERT: A 454 GLN cc_start: 0.9065 (mt0) cc_final: 0.8708 (mt0) REVERT: B 448 LYS cc_start: 0.9337 (mmtp) cc_final: 0.9010 (tppt) REVERT: C 292 MET cc_start: 0.9503 (mtm) cc_final: 0.9208 (mtm) REVERT: C 299 ASP cc_start: 0.9107 (t0) cc_final: 0.8803 (t0) REVERT: C 448 LYS cc_start: 0.9453 (mttt) cc_final: 0.8952 (tppp) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.0849 time to fit residues: 6.5784 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.046949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.035923 restraints weight = 45205.645| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 4.48 r_work: 0.2396 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10491 Z= 0.098 Angle : 0.522 8.940 14301 Z= 0.261 Chirality : 0.043 0.197 1776 Planarity : 0.003 0.032 1812 Dihedral : 4.193 16.072 1425 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.35 % Allowed : 8.25 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1329 helix: 2.12 (0.26), residues: 459 sheet: 0.21 (0.32), residues: 261 loop : -0.42 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.007 0.001 TYR C 270 PHE 0.012 0.001 PHE A 105 TRP 0.001 0.000 TRP A 303 HIS 0.001 0.000 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (10464) covalent geometry : angle 0.50167 / 0.26 (14235) SS BOND : bond 0.00085 / 0.06 ( 15) SS BOND : angle 0.60738 / 0.45 ( 30) hydrogen bonds : bond 0.03001 / 2.06 ( 459) hydrogen bonds : angle 4.23292 / 2.99 ( 1287) link_BETA1-4 : bond 0.01136 / 0.57 ( 6) link_BETA1-4 : angle 2.65572 / 1.66 ( 18) link_NAG-ASN : bond 0.00715 / 0.36 ( 6) link_NAG-ASN : angle 3.12059 / 1.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9497 (tpp) cc_final: 0.9223 (tpp) REVERT: A 110 MET cc_start: 0.9504 (tpt) cc_final: 0.9077 (tpt) REVERT: A 451 ILE cc_start: 0.9336 (tt) cc_final: 0.9027 (pt) REVERT: A 453 ASN cc_start: 0.9397 (m-40) cc_final: 0.9116 (m110) REVERT: A 454 GLN cc_start: 0.8992 (mt0) cc_final: 0.8570 (mt0) REVERT: B 92 MET cc_start: 0.9544 (tpp) cc_final: 0.9246 (tpp) REVERT: B 448 LYS cc_start: 0.9348 (mmtp) cc_final: 0.8997 (tppt) REVERT: C 292 MET cc_start: 0.9511 (mtm) cc_final: 0.9235 (mtm) REVERT: C 299 ASP cc_start: 0.9093 (t0) cc_final: 0.8782 (t0) REVERT: C 448 LYS cc_start: 0.9452 (mttt) cc_final: 0.8941 (tppp) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.0786 time to fit residues: 6.0505 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 12 optimal weight: 0.4980 chunk 42 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 78 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.035887 restraints weight = 44459.904| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 4.41 r_work: 0.2437 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10491 Z= 0.092 Angle : 0.512 9.504 14301 Z= 0.254 Chirality : 0.042 0.202 1776 Planarity : 0.003 0.031 1812 Dihedral : 4.074 15.661 1425 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.43 % Allowed : 8.16 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1329 helix: 2.16 (0.26), residues: 459 sheet: 0.27 (0.32), residues: 261 loop : -0.41 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.039 0.001 TYR C 345 PHE 0.011 0.001 PHE B 277 TRP 0.001 0.000 TRP A 303 HIS 0.002 0.000 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (10464) covalent geometry : angle 0.49151 / 0.25 (14235) SS BOND : bond 0.00084 / 0.06 ( 15) SS BOND : angle 0.54236 / 0.40 ( 30) hydrogen bonds : bond 0.02831 / 1.93 ( 459) hydrogen bonds : angle 4.11716 / 2.90 ( 1287) link_BETA1-4 : bond 0.01148 / 0.57 ( 6) link_BETA1-4 : angle 2.68094 / 1.63 ( 18) link_NAG-ASN : bond 0.00620 / 0.31 ( 6) link_NAG-ASN : angle 3.05178 / 1.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9513 (tpp) cc_final: 0.9286 (tpp) REVERT: A 105 PHE cc_start: 0.8600 (t80) cc_final: 0.8170 (t80) REVERT: A 110 MET cc_start: 0.9476 (tpt) cc_final: 0.9045 (tpt) REVERT: A 451 ILE cc_start: 0.9369 (tt) cc_final: 0.9112 (pt) REVERT: A 453 ASN cc_start: 0.9392 (m-40) cc_final: 0.9136 (m110) REVERT: B 92 MET cc_start: 0.9588 (tpp) cc_final: 0.9277 (tpp) REVERT: B 448 LYS cc_start: 0.9353 (mmtp) cc_final: 0.9004 (tppt) REVERT: C 292 MET cc_start: 0.9516 (mtm) cc_final: 0.9206 (mtm) REVERT: C 299 ASP cc_start: 0.9052 (t0) cc_final: 0.8741 (t0) REVERT: C 448 LYS cc_start: 0.9479 (mttt) cc_final: 0.8990 (tppp) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.0921 time to fit residues: 6.9660 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 343 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN C 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.035547 restraints weight = 44402.524| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.37 r_work: 0.2407 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10491 Z= 0.113 Angle : 0.524 9.017 14301 Z= 0.259 Chirality : 0.042 0.191 1776 Planarity : 0.003 0.031 1812 Dihedral : 4.084 19.692 1425 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.26 % Allowed : 8.59 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1329 helix: 2.19 (0.26), residues: 459 sheet: 0.23 (0.32), residues: 261 loop : -0.41 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.007 0.001 TYR B 249 PHE 0.011 0.001 PHE B 277 TRP 0.001 0.000 TRP A 303 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10464) covalent geometry : angle 0.50574 / 0.25 (14235) SS BOND : bond 0.00116 / 0.08 ( 15) SS BOND : angle 0.57391 / 0.42 ( 30) hydrogen bonds : bond 0.02904 / 1.99 ( 459) hydrogen bonds : angle 4.11632 / 2.91 ( 1287) link_BETA1-4 : bond 0.01023 / 0.51 ( 6) link_BETA1-4 : angle 2.54971 / 1.56 ( 18) link_NAG-ASN : bond 0.00597 / 0.30 ( 6) link_NAG-ASN : angle 2.92097 / 1.77 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9504 (tpp) cc_final: 0.9082 (tpp) REVERT: A 110 MET cc_start: 0.9470 (tpt) cc_final: 0.9032 (tpt) REVERT: A 451 ILE cc_start: 0.9342 (tt) cc_final: 0.9029 (pt) REVERT: A 453 ASN cc_start: 0.9400 (m-40) cc_final: 0.9149 (m110) REVERT: A 454 GLN cc_start: 0.9006 (mt0) cc_final: 0.8581 (mt0) REVERT: B 92 MET cc_start: 0.9547 (tpp) cc_final: 0.9229 (tpp) REVERT: B 448 LYS cc_start: 0.9306 (mmtp) cc_final: 0.8954 (tppt) REVERT: C 292 MET cc_start: 0.9510 (mtm) cc_final: 0.9172 (mtm) REVERT: C 299 ASP cc_start: 0.9105 (t0) cc_final: 0.8795 (t0) REVERT: C 448 LYS cc_start: 0.9466 (mttt) cc_final: 0.8992 (tppp) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.0663 time to fit residues: 4.8660 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 343 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.034203 restraints weight = 46367.590| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 4.45 r_work: 0.2369 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10491 Z= 0.239 Angle : 0.635 9.238 14301 Z= 0.309 Chirality : 0.044 0.183 1776 Planarity : 0.003 0.029 1812 Dihedral : 4.355 16.041 1425 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.26 % Allowed : 8.85 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1329 helix: 2.16 (0.25), residues: 456 sheet: 0.15 (0.32), residues: 261 loop : -0.51 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.010 0.001 TYR B 249 PHE 0.013 0.002 PHE A 105 TRP 0.001 0.000 TRP B 303 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (10464) covalent geometry : angle 0.62157 / 0.31 (14235) SS BOND : bond 0.00262 / 0.16 ( 15) SS BOND : angle 0.84534 / 0.61 ( 30) hydrogen bonds : bond 0.03634 / 2.48 ( 459) hydrogen bonds : angle 4.35009 / 3.09 ( 1287) link_BETA1-4 : bond 0.01003 / 0.49 ( 6) link_BETA1-4 : angle 2.52588 / 1.52 ( 18) link_NAG-ASN : bond 0.00490 / 0.24 ( 6) link_NAG-ASN : angle 2.62045 / 1.58 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.80 seconds wall clock time: 32 minutes 13.70 seconds (1933.70 seconds total)