Starting phenix.real_space_refine on Sat Aug 23 07:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmx_29299/08_2025/8fmx_29299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmx_29299/08_2025/8fmx_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_29299/08_2025/8fmx_29299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmx_29299/08_2025/8fmx_29299.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmx_29299/08_2025/8fmx_29299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmx_29299/08_2025/8fmx_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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.26 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: 1.11 Conformation dependent library (CDL) restraints added in 406.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.46 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: 1.89 Time building geometry restraints manager: 1.43 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 - 21.35: 6232 21.35 - 42.69: 258 42.69 - 64.04: 36 64.04 - 85.39: 35 85.39 - 106.73: 15 Dihedral angle restraints: 6576 sinusoidal: 2700 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 6573 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: 0.03 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.660 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 14.518 106.735 4041 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 aren 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 covalent geometry : bond 0.00481 (10464) covalent geometry : angle 0.93047 (14235) SS BOND : bond 0.00366 ( 15) SS BOND : angle 1.20388 ( 30) hydrogen bonds : bond 0.14068 ( 459) hydrogen bonds : angle 6.69389 ( 1287) link_BETA1-4 : bond 0.01768 ( 6) link_BETA1-4 : angle 5.29334 ( 18) link_NAG-ASN : bond 0.00841 ( 6) link_NAG-ASN : angle 6.82581 ( 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 : 0.426 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: 0.1499 time to fit residues: 18.1213 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 : 0.414 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2888 r_free = 0.2888 target = 0.047419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.036536 restraints weight = 44438.567| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 4.40 r_work: 0.2419 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10491 Z= 0.140 Angle : 0.663 9.876 14301 Z= 0.333 Chirality : 0.047 0.407 1776 Planarity : 0.004 0.052 1812 Dihedral : 9.791 72.474 1671 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 aren not related in a simple way. whole: 0.31 (0.23), residues: 1329 helix: 1.01 (0.24), 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 0.005 0.001 ARG B 232 TYR 0.013 0.001 TYR A 41 PHE 0.016 0.002 PHE C 105 TRP 0.003 0.001 TRP C 303 HIS 0.001 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00298 (10464) covalent geometry : angle 0.62289 (14235) SS BOND : bond 0.00122 ( 15) SS BOND : angle 0.97918 ( 30) hydrogen bonds : bond 0.04554 ( 459) hydrogen bonds : angle 5.11328 ( 1287) link_BETA1-4 : bond 0.01615 ( 6) link_BETA1-4 : angle 3.52587 ( 18) link_NAG-ASN : bond 0.00629 ( 6) link_NAG-ASN : angle 5.35219 ( 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 : 0.413 Fit side-chains revert: symmetry clash REVERT: A 453 ASN cc_start: 0.9249 (m-40) cc_final: 0.8957 (m110) REVERT: A 454 GLN cc_start: 0.8968 (mt0) cc_final: 0.8665 (mp10) REVERT: B 92 MET cc_start: 0.9578 (tpp) cc_final: 0.9118 (tpp) REVERT: C 92 MET cc_start: 0.9638 (tpp) cc_final: 0.9141 (tpp) REVERT: C 110 MET cc_start: 0.9247 (tpp) cc_final: 0.9026 (tpt) REVERT: C 448 LYS cc_start: 0.9418 (mttt) cc_final: 0.8979 (tppp) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.0899 time to fit residues: 8.7704 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.0870 chunk 104 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.0470 chunk 124 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.047598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.036341 restraints weight = 44808.997| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 4.46 r_work: 0.2440 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10491 Z= 0.105 Angle : 0.565 9.226 14301 Z= 0.284 Chirality : 0.044 0.232 1776 Planarity : 0.003 0.036 1812 Dihedral : 6.996 51.415 1671 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.95 % Allowed : 5.47 % Favored : 93.58 % 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 aren not related in a simple way. whole: 0.65 (0.23), residues: 1329 helix: 1.66 (0.26), 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 0.007 0.001 TYR A 41 PHE 0.012 0.001 PHE B 277 TRP 0.001 0.001 TRP C 303 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00216 (10464) covalent geometry : angle 0.52966 (14235) SS BOND : bond 0.00085 ( 15) SS BOND : angle 0.67504 ( 30) hydrogen bonds : bond 0.03631 ( 459) hydrogen bonds : angle 4.74101 ( 1287) link_BETA1-4 : bond 0.01305 ( 6) link_BETA1-4 : angle 3.23246 ( 18) link_NAG-ASN : bond 0.00953 ( 6) link_NAG-ASN : angle 4.54784 ( 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 64 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.442 Fit side-chains REVERT: A 100 ASN cc_start: 0.8975 (t0) cc_final: 0.8523 (p0) REVERT: A 453 ASN cc_start: 0.9379 (m-40) cc_final: 0.9025 (m110) REVERT: A 454 GLN cc_start: 0.8978 (mt0) cc_final: 0.8657 (pt0) REVERT: B 92 MET cc_start: 0.9565 (tpp) cc_final: 0.9186 (tpp) REVERT: B 448 LYS cc_start: 0.9333 (mmtp) cc_final: 0.9077 (mmtp) REVERT: C 110 MET cc_start: 0.9099 (tpp) cc_final: 0.8837 (tpp) REVERT: C 292 MET cc_start: 0.9420 (mtm) cc_final: 0.9105 (mtm) REVERT: C 343 MET cc_start: 0.8279 (mtm) cc_final: 0.7815 (mpp) REVERT: C 448 LYS cc_start: 0.9505 (mttt) cc_final: 0.9015 (tppp) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.1032 time to fit residues: 9.5379 Evaluate side-chains 49 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 245 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.048235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.037366 restraints weight = 45113.051| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 4.39 r_work: 0.2421 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10491 Z= 0.100 Angle : 0.542 9.007 14301 Z= 0.269 Chirality : 0.043 0.206 1776 Planarity : 0.003 0.047 1812 Dihedral : 5.689 51.192 1671 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.04 % Allowed : 5.82 % 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 aren not related in a simple way. whole: 0.75 (0.23), residues: 1329 helix: 1.85 (0.26), residues: 456 sheet: 0.33 (0.33), residues: 258 loop : -0.42 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.006 0.001 TYR C 415 PHE 0.009 0.001 PHE A 277 TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00217 (10464) covalent geometry : angle 0.50863 (14235) SS BOND : bond 0.00094 ( 15) SS BOND : angle 0.56581 ( 30) hydrogen bonds : bond 0.03206 ( 459) hydrogen bonds : angle 4.50089 ( 1287) link_BETA1-4 : bond 0.01323 ( 6) link_BETA1-4 : angle 3.10331 ( 18) link_NAG-ASN : bond 0.00866 ( 6) link_NAG-ASN : angle 4.32802 ( 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: 12 poor density : 50 time to evaluate : 0.449 Fit side-chains REVERT: A 92 MET cc_start: 0.9487 (tpp) cc_final: 0.9167 (tpp) REVERT: A 105 PHE cc_start: 0.8397 (t80) cc_final: 0.8015 (t80) REVERT: A 110 MET cc_start: 0.9498 (tpt) cc_final: 0.9161 (tpt) REVERT: A 453 ASN cc_start: 0.9364 (m-40) cc_final: 0.9070 (m110) REVERT: A 454 GLN cc_start: 0.9014 (mt0) cc_final: 0.8727 (pt0) REVERT: B 92 MET cc_start: 0.9535 (tpp) cc_final: 0.9208 (tpp) REVERT: B 448 LYS cc_start: 0.9355 (mmtp) cc_final: 0.9028 (mmtp) REVERT: C 92 MET cc_start: 0.9595 (tpp) cc_final: 0.9102 (tpp) REVERT: C 110 MET cc_start: 0.9097 (tpp) cc_final: 0.8806 (tpp) REVERT: C 292 MET cc_start: 0.9421 (mtm) cc_final: 0.9084 (mtm) REVERT: C 343 MET cc_start: 0.8254 (mtm) cc_final: 0.7630 (mpp) REVERT: C 448 LYS cc_start: 0.9507 (mttt) cc_final: 0.9018 (tppp) outliers start: 12 outliers final: 2 residues processed: 61 average time/residue: 0.0897 time to fit residues: 8.7419 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 SER 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: 2.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.046908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.035734 restraints weight = 45404.870| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 4.46 r_work: 0.2414 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10491 Z= 0.144 Angle : 0.552 8.664 14301 Z= 0.276 Chirality : 0.043 0.192 1776 Planarity : 0.003 0.033 1812 Dihedral : 5.506 50.553 1671 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.87 % Allowed : 6.16 % Favored : 92.97 % 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 aren not related in a simple way. whole: 0.76 (0.23), residues: 1329 helix: 1.94 (0.26), residues: 456 sheet: 0.31 (0.32), residues: 258 loop : -0.48 (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 B 249 PHE 0.009 0.001 PHE A 277 TRP 0.002 0.000 TRP B 303 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00327 (10464) covalent geometry : angle 0.52478 (14235) SS BOND : bond 0.00153 ( 15) SS BOND : angle 0.64973 ( 30) hydrogen bonds : bond 0.03313 ( 459) hydrogen bonds : angle 4.43913 ( 1287) link_BETA1-4 : bond 0.01226 ( 6) link_BETA1-4 : angle 2.84638 ( 18) link_NAG-ASN : bond 0.00731 ( 6) link_NAG-ASN : angle 3.97056 ( 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 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9542 (tpp) cc_final: 0.9011 (tpp) REVERT: A 105 PHE cc_start: 0.8428 (t80) cc_final: 0.8034 (t80) REVERT: A 110 MET cc_start: 0.9534 (tpt) cc_final: 0.9205 (tpt) REVERT: A 453 ASN cc_start: 0.9386 (m-40) cc_final: 0.9078 (m110) REVERT: A 454 GLN cc_start: 0.8893 (mt0) cc_final: 0.8532 (mt0) REVERT: B 92 MET cc_start: 0.9584 (tpp) cc_final: 0.9232 (tpp) REVERT: B 448 LYS cc_start: 0.9375 (mmtp) cc_final: 0.8823 (tppt) REVERT: C 292 MET cc_start: 0.9454 (mtm) cc_final: 0.9158 (mtm) REVERT: C 299 ASP cc_start: 0.9047 (t0) cc_final: 0.8742 (t0) REVERT: C 448 LYS cc_start: 0.9500 (mttt) cc_final: 0.9099 (tppp) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.0967 time to fit residues: 8.0460 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 22 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.046357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.035678 restraints weight = 45931.101| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 4.36 r_work: 0.2398 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10491 Z= 0.177 Angle : 0.565 8.320 14301 Z= 0.280 Chirality : 0.043 0.179 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.418 50.372 1671 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.61 % Allowed : 6.86 % Favored : 92.53 % 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 aren not related in a simple way. whole: 0.72 (0.23), residues: 1329 helix: 1.93 (0.25), residues: 456 sheet: 0.22 (0.32), residues: 261 loop : -0.48 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.008 0.001 TYR B 249 PHE 0.008 0.001 PHE A 277 TRP 0.002 0.001 TRP A 303 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00406 (10464) covalent geometry : angle 0.54102 (14235) SS BOND : bond 0.00179 ( 15) SS BOND : angle 0.72584 ( 30) hydrogen bonds : bond 0.03410 ( 459) hydrogen bonds : angle 4.41864 ( 1287) link_BETA1-4 : bond 0.01137 ( 6) link_BETA1-4 : angle 2.65022 ( 18) link_NAG-ASN : bond 0.00704 ( 6) link_NAG-ASN : angle 3.77939 ( 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 51 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9567 (tpp) cc_final: 0.9015 (tpp) REVERT: A 105 PHE cc_start: 0.8413 (t80) cc_final: 0.8093 (t80) REVERT: A 110 MET cc_start: 0.9533 (tpt) cc_final: 0.9191 (tpt) REVERT: A 453 ASN cc_start: 0.9374 (m-40) cc_final: 0.9099 (m110) REVERT: A 454 GLN cc_start: 0.9051 (mt0) cc_final: 0.8683 (mt0) REVERT: B 448 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8962 (tppt) REVERT: C 292 MET cc_start: 0.9460 (mtm) cc_final: 0.9178 (mtm) REVERT: C 299 ASP cc_start: 0.9063 (t0) cc_final: 0.8742 (t0) REVERT: C 448 LYS cc_start: 0.9487 (mttt) cc_final: 0.9050 (tppp) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.0979 time to fit residues: 7.5587 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.044527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.033577 restraints weight = 45427.037| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 4.42 r_work: 0.2363 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10491 Z= 0.232 Angle : 0.616 7.848 14301 Z= 0.303 Chirality : 0.044 0.173 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.501 49.756 1671 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.69 % Allowed : 7.47 % Favored : 91.84 % 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 aren not related in a simple way. whole: 0.66 (0.23), residues: 1329 helix: 1.93 (0.25), residues: 456 sheet: 0.10 (0.32), residues: 261 loop : -0.52 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 232 TYR 0.010 0.001 TYR B 249 PHE 0.010 0.001 PHE A 234 TRP 0.002 0.001 TRP B 303 HIS 0.005 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00530 (10464) covalent geometry : angle 0.59692 (14235) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.85643 ( 30) hydrogen bonds : bond 0.03678 ( 459) hydrogen bonds : angle 4.52001 ( 1287) link_BETA1-4 : bond 0.01202 ( 6) link_BETA1-4 : angle 2.58613 ( 18) link_NAG-ASN : bond 0.00659 ( 6) link_NAG-ASN : angle 3.50102 ( 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: 8 poor density : 42 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9561 (tpp) cc_final: 0.9012 (tpp) REVERT: A 110 MET cc_start: 0.9523 (tpt) cc_final: 0.9129 (tpt) REVERT: A 453 ASN cc_start: 0.9379 (m-40) cc_final: 0.9078 (m110) REVERT: A 454 GLN cc_start: 0.9048 (mt0) cc_final: 0.8718 (mt0) REVERT: B 92 MET cc_start: 0.9565 (tpp) cc_final: 0.9224 (tpp) REVERT: B 448 LYS cc_start: 0.9348 (mmtp) cc_final: 0.8815 (tppt) REVERT: C 292 MET cc_start: 0.9507 (mtm) cc_final: 0.9235 (mtm) REVERT: C 299 ASP cc_start: 0.9110 (t0) cc_final: 0.8811 (t0) REVERT: C 448 LYS cc_start: 0.9459 (mttt) cc_final: 0.9007 (tppp) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0939 time to fit residues: 7.2151 Evaluate side-chains 45 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU 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: 6.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.045295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.034281 restraints weight = 44976.838| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 4.40 r_work: 0.2389 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10491 Z= 0.147 Angle : 0.558 10.268 14301 Z= 0.277 Chirality : 0.043 0.192 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.367 50.666 1671 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.52 % Allowed : 8.16 % Favored : 91.32 % 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 aren not related in a simple way. whole: 0.69 (0.23), residues: 1329 helix: 1.96 (0.25), residues: 459 sheet: 0.11 (0.32), residues: 261 loop : -0.52 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.009 0.001 TYR B 249 PHE 0.011 0.001 PHE A 105 TRP 0.002 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00337 (10464) covalent geometry : angle 0.53661 (14235) SS BOND : bond 0.00155 ( 15) SS BOND : angle 0.72772 ( 30) hydrogen bonds : bond 0.03407 ( 459) hydrogen bonds : angle 4.35356 ( 1287) link_BETA1-4 : bond 0.01132 ( 6) link_BETA1-4 : angle 2.57231 ( 18) link_NAG-ASN : bond 0.00739 ( 6) link_NAG-ASN : angle 3.47970 ( 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: 6 poor density : 44 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9544 (tpp) cc_final: 0.9024 (tpp) REVERT: A 110 MET cc_start: 0.9527 (tpt) cc_final: 0.9128 (tpt) REVERT: A 451 ILE cc_start: 0.9319 (tt) cc_final: 0.8990 (pt) REVERT: A 453 ASN cc_start: 0.9383 (m-40) cc_final: 0.9094 (m110) REVERT: A 454 GLN cc_start: 0.9056 (mt0) cc_final: 0.8639 (mt0) REVERT: B 92 MET cc_start: 0.9583 (tpp) cc_final: 0.9224 (tpp) REVERT: B 448 LYS cc_start: 0.9325 (mmtp) cc_final: 0.8904 (tppt) REVERT: C 92 MET cc_start: 0.9602 (tpp) cc_final: 0.9140 (tpp) REVERT: C 292 MET cc_start: 0.9502 (mtm) cc_final: 0.9237 (mtm) REVERT: C 448 LYS cc_start: 0.9468 (mttt) cc_final: 0.9005 (tppp) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.0977 time to fit residues: 7.2451 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 306 LEU 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: 0.8980 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.034577 restraints weight = 44886.044| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.40 r_work: 0.2414 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10491 Z= 0.118 Angle : 0.531 9.464 14301 Z= 0.264 Chirality : 0.042 0.187 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.202 51.280 1671 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.35 % Allowed : 8.94 % Favored : 90.71 % 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 aren not related in a simple way. whole: 0.80 (0.24), residues: 1329 helix: 2.07 (0.26), residues: 459 sheet: 0.17 (0.32), residues: 261 loop : -0.47 (0.25), residues: 609 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 A 105 TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00269 (10464) covalent geometry : angle 0.50906 (14235) SS BOND : bond 0.00116 ( 15) SS BOND : angle 0.65307 ( 30) hydrogen bonds : bond 0.03100 ( 459) hydrogen bonds : angle 4.25924 ( 1287) link_BETA1-4 : bond 0.01124 ( 6) link_BETA1-4 : angle 2.53173 ( 18) link_NAG-ASN : bond 0.00720 ( 6) link_NAG-ASN : angle 3.41246 ( 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 53 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9533 (tpp) cc_final: 0.9055 (tpp) REVERT: A 110 MET cc_start: 0.9492 (tpt) cc_final: 0.9085 (tpt) REVERT: A 451 ILE cc_start: 0.9345 (tt) cc_final: 0.9035 (pt) REVERT: A 454 GLN cc_start: 0.9064 (mt0) cc_final: 0.8627 (mt0) REVERT: B 92 MET cc_start: 0.9577 (tpp) cc_final: 0.9227 (tpp) REVERT: C 92 MET cc_start: 0.9602 (tpp) cc_final: 0.9136 (tpp) REVERT: C 110 MET cc_start: 0.9361 (ttm) cc_final: 0.9149 (ttm) REVERT: C 292 MET cc_start: 0.9506 (mtm) cc_final: 0.9237 (mtm) REVERT: C 299 ASP cc_start: 0.9051 (t0) cc_final: 0.8733 (t0) REVERT: C 448 LYS cc_start: 0.9472 (mttt) cc_final: 0.8925 (tppt) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.0767 time to fit residues: 6.3624 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.035088 restraints weight = 44444.490| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.37 r_work: 0.2434 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10491 Z= 0.103 Angle : 0.522 9.502 14301 Z= 0.260 Chirality : 0.042 0.194 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.132 51.051 1671 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.17 % Allowed : 9.11 % Favored : 90.71 % 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 aren not related in a simple way. whole: 0.86 (0.24), residues: 1329 helix: 2.13 (0.26), residues: 459 sheet: 0.21 (0.32), residues: 261 loop : -0.46 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.037 0.001 TYR C 345 PHE 0.012 0.001 PHE A 105 TRP 0.002 0.000 TRP B 303 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00231 (10464) covalent geometry : angle 0.49977 (14235) SS BOND : bond 0.00092 ( 15) SS BOND : angle 0.61135 ( 30) hydrogen bonds : bond 0.02972 ( 459) hydrogen bonds : angle 4.16831 ( 1287) link_BETA1-4 : bond 0.00991 ( 6) link_BETA1-4 : angle 2.70256 ( 18) link_NAG-ASN : bond 0.00698 ( 6) link_NAG-ASN : angle 3.38307 ( 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 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9531 (tpp) cc_final: 0.9098 (tpp) REVERT: A 110 MET cc_start: 0.9486 (tpt) cc_final: 0.9090 (tpt) REVERT: A 451 ILE cc_start: 0.9347 (tt) cc_final: 0.9033 (pt) REVERT: A 453 ASN cc_start: 0.9395 (m-40) cc_final: 0.9136 (m110) REVERT: A 454 GLN cc_start: 0.8996 (mt0) cc_final: 0.8578 (mt0) REVERT: B 92 MET cc_start: 0.9568 (tpp) cc_final: 0.9217 (tpp) REVERT: B 448 LYS cc_start: 0.9290 (mmtp) cc_final: 0.8781 (tppt) REVERT: C 92 MET cc_start: 0.9600 (tpp) cc_final: 0.9114 (tpp) REVERT: C 110 MET cc_start: 0.9371 (ttm) cc_final: 0.9164 (ttm) REVERT: C 292 MET cc_start: 0.9506 (mtm) cc_final: 0.9228 (mtm) REVERT: C 299 ASP cc_start: 0.9084 (t0) cc_final: 0.8770 (t0) REVERT: C 448 LYS cc_start: 0.9463 (mttt) cc_final: 0.9013 (tppp) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.0905 time to fit residues: 6.6806 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 454 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 0.0060 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.033886 restraints weight = 45624.242| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 4.38 r_work: 0.2391 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10491 Z= 0.180 Angle : 0.574 9.324 14301 Z= 0.282 Chirality : 0.043 0.195 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.171 50.246 1671 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.35 % Allowed : 8.85 % Favored : 90.80 % 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 aren not related in a simple way. whole: 0.81 (0.24), residues: 1329 helix: 2.16 (0.26), residues: 456 sheet: 0.14 (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 B 232 TYR 0.020 0.001 TYR A 345 PHE 0.012 0.001 PHE A 105 TRP 0.002 0.000 TRP B 303 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00411 (10464) covalent geometry : angle 0.55580 (14235) SS BOND : bond 0.00203 ( 15) SS BOND : angle 0.75774 ( 30) hydrogen bonds : bond 0.03310 ( 459) hydrogen bonds : angle 4.27133 ( 1287) link_BETA1-4 : bond 0.01045 ( 6) link_BETA1-4 : angle 2.39871 ( 18) link_NAG-ASN : bond 0.00586 ( 6) link_NAG-ASN : angle 3.22632 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.89 seconds wall clock time: 34 minutes 14.96 seconds (2054.96 seconds total)