Starting phenix.real_space_refine on Mon Jun 9 10:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmx_29299/06_2025/8fmx_29299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmx_29299/06_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_29299/06_2025/8fmx_29299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmx_29299/06_2025/8fmx_29299.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmx_29299/06_2025/8fmx_29299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmx_29299/06_2025/8fmx_29299.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.97, per 1000 atoms: 0.77 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: 2.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.31 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: 4.08 Time building geometry restraints manager: 3.31 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: 0.06 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: 63.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), 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 TRP 0.013 0.002 TRP B 303 HIS 0.005 0.002 HIS C 130 PHE 0.023 0.003 PHE C 234 TYR 0.030 0.006 TYR B 201 ARG 0.012 0.002 ARG B 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 6) link_NAG-ASN : angle 6.82581 ( 18) link_BETA1-4 : bond 0.01768 ( 6) link_BETA1-4 : angle 5.29334 ( 18) hydrogen bonds : bond 0.14068 ( 459) hydrogen bonds : angle 6.69389 ( 1287) SS BOND : bond 0.00366 ( 15) SS BOND : angle 1.20388 ( 30) covalent geometry : bond 0.00481 (10464) covalent geometry : angle 0.93047 (14235) *********************** 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 : 1.326 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: 0.3374 time to fit residues: 41.0534 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 : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.2805 r_free = 0.2805 target = 0.044334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.033504 restraints weight = 45434.508| |-----------------------------------------------------------------------------| r_work (start): 0.2487 rms_B_bonded: 4.32 r_work: 0.2337 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10491 Z= 0.315 Angle : 0.785 9.285 14301 Z= 0.388 Chirality : 0.049 0.380 1776 Planarity : 0.004 0.056 1812 Dihedral : 10.283 77.412 1671 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.87 % Allowed : 4.43 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1329 helix: 0.92 (0.24), residues: 456 sheet: 0.18 (0.32), residues: 261 loop : -0.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.006 0.002 HIS A 130 PHE 0.020 0.002 PHE C 105 TYR 0.014 0.002 TYR A 41 ARG 0.005 0.001 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 6) link_NAG-ASN : angle 5.17976 ( 18) link_BETA1-4 : bond 0.01591 ( 6) link_BETA1-4 : angle 3.57108 ( 18) hydrogen bonds : bond 0.05011 ( 459) hydrogen bonds : angle 5.26551 ( 1287) SS BOND : bond 0.00306 ( 15) SS BOND : angle 1.21384 ( 30) covalent geometry : bond 0.00721 (10464) covalent geometry : angle 0.75233 (14235) *********************** 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 58 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 1.170 Fit side-chains REVERT: A 92 MET cc_start: 0.9658 (tpp) cc_final: 0.9457 (tpp) REVERT: A 241 MET cc_start: 0.9238 (mtm) cc_final: 0.9027 (mtm) REVERT: A 453 ASN cc_start: 0.9265 (m-40) cc_final: 0.9006 (m110) REVERT: A 454 GLN cc_start: 0.9018 (mt0) cc_final: 0.8578 (mt0) REVERT: B 92 MET cc_start: 0.9631 (tpp) cc_final: 0.9333 (tpp) REVERT: B 448 LYS cc_start: 0.9369 (mmtp) cc_final: 0.9147 (mmtp) REVERT: C 92 MET cc_start: 0.9684 (tpp) cc_final: 0.9134 (tpp) REVERT: C 110 MET cc_start: 0.9302 (tpp) cc_final: 0.9024 (tpp) REVERT: C 448 LYS cc_start: 0.9457 (mttt) cc_final: 0.9021 (tppp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.2043 time to fit residues: 16.8183 Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 240 ILE 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 128 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 123 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.045119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.034116 restraints weight = 45058.505| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 4.37 r_work: 0.2388 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2143 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= 0.134 Angle : 0.588 8.883 14301 Z= 0.295 Chirality : 0.045 0.241 1776 Planarity : 0.003 0.036 1812 Dihedral : 7.303 51.205 1671 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.87 % Allowed : 5.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1329 helix: 1.65 (0.25), residues: 456 sheet: 0.27 (0.33), residues: 258 loop : -0.58 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.001 PHE B 277 TYR 0.008 0.001 TYR C 270 ARG 0.004 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 6) link_NAG-ASN : angle 4.48282 ( 18) link_BETA1-4 : bond 0.01499 ( 6) link_BETA1-4 : angle 3.27868 ( 18) hydrogen bonds : bond 0.03832 ( 459) hydrogen bonds : angle 4.77695 ( 1287) SS BOND : bond 0.00104 ( 15) SS BOND : angle 0.84929 ( 30) covalent geometry : bond 0.00297 (10464) covalent geometry : angle 0.55388 (14235) *********************** 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: 10 poor density : 50 time to evaluate : 1.045 Fit side-chains REVERT: A 453 ASN cc_start: 0.9359 (m-40) cc_final: 0.9028 (m110) REVERT: A 454 GLN cc_start: 0.8978 (mt0) cc_final: 0.8629 (mt0) REVERT: C 92 MET cc_start: 0.9645 (tpp) cc_final: 0.9209 (tpp) REVERT: C 110 MET cc_start: 0.9128 (tpp) cc_final: 0.8844 (tpp) REVERT: C 448 LYS cc_start: 0.9494 (mttt) cc_final: 0.9016 (tppp) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.1967 time to fit residues: 18.3747 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 : 1.290 ------------------------------------------------------------------------------- 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 B residue 367 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.4182 ------------------------------------------------------------------------------- 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 = 0.2822 r_free = 0.2822 target = 0.044729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.033723 restraints weight = 44767.605| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 4.39 r_work: 0.2366 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10491 Z= 0.199 Angle : 0.610 8.294 14301 Z= 0.302 Chirality : 0.044 0.217 1776 Planarity : 0.003 0.037 1812 Dihedral : 6.181 49.823 1671 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.22 % Allowed : 6.16 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1329 helix: 1.78 (0.25), residues: 456 sheet: 0.17 (0.32), residues: 258 loop : -0.60 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 303 HIS 0.005 0.001 HIS A 130 PHE 0.010 0.001 PHE A 277 TYR 0.009 0.001 TYR C 249 ARG 0.003 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 6) link_NAG-ASN : angle 4.02950 ( 18) link_BETA1-4 : bond 0.01323 ( 6) link_BETA1-4 : angle 3.16048 ( 18) hydrogen bonds : bond 0.03852 ( 459) hydrogen bonds : angle 4.63381 ( 1287) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.82556 ( 30) covalent geometry : bond 0.00454 (10464) covalent geometry : angle 0.58268 (14235) *********************** 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 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 1.165 Fit side-chains REVERT: A 453 ASN cc_start: 0.9314 (m-40) cc_final: 0.8962 (m110) REVERT: A 454 GLN cc_start: 0.8987 (mt0) cc_final: 0.8647 (mt0) REVERT: B 92 MET cc_start: 0.9577 (tpp) cc_final: 0.9189 (tpp) REVERT: B 448 LYS cc_start: 0.9339 (mmtp) cc_final: 0.9002 (mmtt) REVERT: C 92 MET cc_start: 0.9657 (tpp) cc_final: 0.9227 (tpp) REVERT: C 110 MET cc_start: 0.9202 (tpp) cc_final: 0.8910 (tpp) REVERT: C 343 MET cc_start: 0.8477 (mtm) cc_final: 0.7998 (mpp) REVERT: C 448 LYS cc_start: 0.9504 (mttt) cc_final: 0.9113 (tppp) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 0.1987 time to fit residues: 16.9641 Evaluate side-chains 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 257 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.0270 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.2044 ------------------------------------------------------------------------------- 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 = 0.2825 r_free = 0.2825 target = 0.044461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.033465 restraints weight = 45061.593| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 4.34 r_work: 0.2372 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10491 Z= 0.179 Angle : 0.581 8.273 14301 Z= 0.290 Chirality : 0.044 0.197 1776 Planarity : 0.003 0.033 1812 Dihedral : 5.891 50.170 1671 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.87 % Allowed : 6.94 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1329 helix: 1.89 (0.25), residues: 456 sheet: 0.10 (0.32), residues: 261 loop : -0.57 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 303 HIS 0.004 0.001 HIS A 130 PHE 0.011 0.001 PHE B 277 TYR 0.007 0.001 TYR C 249 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 6) link_NAG-ASN : angle 3.88831 ( 18) link_BETA1-4 : bond 0.01333 ( 6) link_BETA1-4 : angle 2.98396 ( 18) hydrogen bonds : bond 0.03637 ( 459) hydrogen bonds : angle 4.54996 ( 1287) SS BOND : bond 0.00197 ( 15) SS BOND : angle 0.81459 ( 30) covalent geometry : bond 0.00409 (10464) covalent geometry : angle 0.55456 (14235) *********************** 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 52 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 1.142 Fit side-chains REVERT: A 453 ASN cc_start: 0.9340 (m-40) cc_final: 0.9032 (m110) REVERT: A 454 GLN cc_start: 0.9022 (mt0) cc_final: 0.8659 (mt0) REVERT: B 448 LYS cc_start: 0.9398 (mmtp) cc_final: 0.8799 (tppt) REVERT: C 92 MET cc_start: 0.9645 (tpp) cc_final: 0.9251 (tpp) REVERT: C 110 MET cc_start: 0.9143 (tpp) cc_final: 0.8871 (tpp) REVERT: C 299 ASP cc_start: 0.9070 (t0) cc_final: 0.8814 (t0) REVERT: C 343 MET cc_start: 0.8617 (mtm) cc_final: 0.8075 (mpp) REVERT: C 448 LYS cc_start: 0.9500 (mttt) cc_final: 0.9051 (tppp) outliers start: 10 outliers final: 3 residues processed: 50 average time/residue: 0.1981 time to fit residues: 15.6285 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.2840 r_free = 0.2840 target = 0.044965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.033925 restraints weight = 45100.544| |-----------------------------------------------------------------------------| r_work (start): 0.2531 rms_B_bonded: 4.38 r_work: 0.2391 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 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 : 0.003 0.029 10491 Z= 0.136 Angle : 0.542 8.090 14301 Z= 0.271 Chirality : 0.043 0.180 1776 Planarity : 0.003 0.035 1812 Dihedral : 5.555 50.941 1671 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.61 % Allowed : 7.20 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1329 helix: 2.03 (0.26), residues: 456 sheet: 0.11 (0.32), residues: 261 loop : -0.45 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE A 105 TYR 0.007 0.001 TYR C 249 ARG 0.002 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 6) link_NAG-ASN : angle 3.77261 ( 18) link_BETA1-4 : bond 0.01215 ( 6) link_BETA1-4 : angle 2.82898 ( 18) hydrogen bonds : bond 0.03307 ( 459) hydrogen bonds : angle 4.39945 ( 1287) SS BOND : bond 0.00146 ( 15) SS BOND : angle 0.70525 ( 30) covalent geometry : bond 0.00309 (10464) covalent geometry : angle 0.51557 (14235) *********************** 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: 7 poor density : 45 time to evaluate : 1.147 Fit side-chains REVERT: A 92 MET cc_start: 0.9560 (tpp) cc_final: 0.9026 (tpp) REVERT: A 110 MET cc_start: 0.9583 (tpt) cc_final: 0.9198 (tpt) REVERT: A 453 ASN cc_start: 0.9359 (m-40) cc_final: 0.9073 (m110) REVERT: A 454 GLN cc_start: 0.9027 (mt0) cc_final: 0.8684 (mt0) REVERT: B 92 MET cc_start: 0.9570 (tpp) cc_final: 0.9219 (tpp) REVERT: B 448 LYS cc_start: 0.9373 (mmtp) cc_final: 0.9038 (tppt) REVERT: C 92 MET cc_start: 0.9628 (tpp) cc_final: 0.9250 (tpp) REVERT: C 110 MET cc_start: 0.9088 (tpp) cc_final: 0.8832 (tpp) REVERT: C 299 ASP cc_start: 0.9117 (t0) cc_final: 0.8817 (t0) REVERT: C 448 LYS cc_start: 0.9490 (mttt) cc_final: 0.8989 (tppp) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.2020 time to fit residues: 15.9042 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.0670 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 chunk 42 optimal weight: 0.0570 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.2865 r_free = 0.2865 target = 0.045821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.034838 restraints weight = 44897.433| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 4.39 r_work: 0.2423 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2963 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= 0.096 Angle : 0.517 9.122 14301 Z= 0.261 Chirality : 0.043 0.183 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.381 51.434 1671 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.35 % Allowed : 7.90 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1329 helix: 2.17 (0.26), residues: 456 sheet: 0.20 (0.32), residues: 261 loop : -0.37 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.001 0.000 HIS A 130 PHE 0.010 0.001 PHE B 277 TYR 0.011 0.001 TYR A 345 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 6) link_NAG-ASN : angle 3.73880 ( 18) link_BETA1-4 : bond 0.01274 ( 6) link_BETA1-4 : angle 2.75840 ( 18) hydrogen bonds : bond 0.03042 ( 459) hydrogen bonds : angle 4.22357 ( 1287) SS BOND : bond 0.00084 ( 15) SS BOND : angle 0.61278 ( 30) covalent geometry : bond 0.00208 (10464) covalent geometry : angle 0.49071 (14235) *********************** 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 52 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.357 Fit side-chains REVERT: A 92 MET cc_start: 0.9532 (tpp) cc_final: 0.9243 (tpp) REVERT: A 110 MET cc_start: 0.9548 (tpt) cc_final: 0.9131 (tpt) REVERT: A 451 ILE cc_start: 0.9368 (tt) cc_final: 0.9072 (pt) REVERT: A 453 ASN cc_start: 0.9374 (m-40) cc_final: 0.9088 (m110) REVERT: A 454 GLN cc_start: 0.9005 (mt0) cc_final: 0.8593 (mt0) REVERT: B 92 MET cc_start: 0.9581 (tpp) cc_final: 0.9222 (tpp) REVERT: B 448 LYS cc_start: 0.9362 (mmtp) cc_final: 0.8848 (tppt) REVERT: C 92 MET cc_start: 0.9617 (tpp) cc_final: 0.9266 (tpp) REVERT: C 110 MET cc_start: 0.9064 (tpp) cc_final: 0.8835 (tpp) REVERT: C 299 ASP cc_start: 0.9079 (t0) cc_final: 0.8767 (t0) REVERT: C 448 LYS cc_start: 0.9465 (mttt) cc_final: 0.8994 (tppp) outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.2749 time to fit residues: 23.5480 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 : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 88 optimal weight: 10.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.2858 r_free = 0.2858 target = 0.045482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.034649 restraints weight = 44743.079| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 4.36 r_work: 0.2418 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10491 Z= 0.114 Angle : 0.521 9.482 14301 Z= 0.260 Chirality : 0.042 0.196 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.262 51.183 1671 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.17 % Allowed : 8.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1329 helix: 2.19 (0.26), residues: 456 sheet: 0.22 (0.32), residues: 261 loop : -0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.002 0.001 HIS C 130 PHE 0.009 0.001 PHE A 105 TYR 0.011 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 6) link_NAG-ASN : angle 3.61523 ( 18) link_BETA1-4 : bond 0.01155 ( 6) link_BETA1-4 : angle 2.63604 ( 18) hydrogen bonds : bond 0.03097 ( 459) hydrogen bonds : angle 4.20719 ( 1287) SS BOND : bond 0.00115 ( 15) SS BOND : angle 0.60174 ( 30) covalent geometry : bond 0.00257 (10464) covalent geometry : angle 0.49677 (14235) *********************** 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 47 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.346 Fit side-chains REVERT: A 92 MET cc_start: 0.9547 (tpp) cc_final: 0.9069 (tpp) REVERT: A 110 MET cc_start: 0.9540 (tpt) cc_final: 0.9155 (tpt) REVERT: A 453 ASN cc_start: 0.9382 (m-40) cc_final: 0.9109 (m110) REVERT: A 454 GLN cc_start: 0.8978 (mt0) cc_final: 0.8647 (mt0) REVERT: B 92 MET cc_start: 0.9587 (tpp) cc_final: 0.9218 (tpp) REVERT: B 448 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8845 (tppt) REVERT: C 92 MET cc_start: 0.9624 (tpp) cc_final: 0.9271 (tpp) REVERT: C 110 MET cc_start: 0.9094 (tpp) cc_final: 0.8849 (tpp) REVERT: C 299 ASP cc_start: 0.9108 (t0) cc_final: 0.8796 (t0) REVERT: C 448 LYS cc_start: 0.9476 (mttt) cc_final: 0.9018 (tppp) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.3028 time to fit residues: 22.0834 Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.2862 r_free = 0.2862 target = 0.045536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.034605 restraints weight = 45471.119| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 4.41 r_work: 0.2419 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3172 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= 0.114 Angle : 0.516 8.906 14301 Z= 0.258 Chirality : 0.042 0.197 1776 Planarity : 0.003 0.030 1812 Dihedral : 5.142 51.313 1671 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.17 % Allowed : 8.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1329 helix: 2.28 (0.26), residues: 456 sheet: 0.25 (0.32), residues: 261 loop : -0.37 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.002 0.001 HIS A 130 PHE 0.012 0.001 PHE A 105 TYR 0.012 0.001 TYR A 345 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 6) link_NAG-ASN : angle 3.47410 ( 18) link_BETA1-4 : bond 0.01094 ( 6) link_BETA1-4 : angle 2.53706 ( 18) hydrogen bonds : bond 0.03037 ( 459) hydrogen bonds : angle 4.16350 ( 1287) SS BOND : bond 0.00108 ( 15) SS BOND : angle 0.60019 ( 30) covalent geometry : bond 0.00258 (10464) covalent geometry : angle 0.49301 (14235) *********************** 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 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9558 (tpp) cc_final: 0.9094 (tpp) REVERT: A 110 MET cc_start: 0.9520 (tpt) cc_final: 0.9145 (tpt) REVERT: A 451 ILE cc_start: 0.9340 (tt) cc_final: 0.9080 (pt) REVERT: A 454 GLN cc_start: 0.8989 (mt0) cc_final: 0.8562 (mt0) REVERT: B 92 MET cc_start: 0.9585 (tpp) cc_final: 0.9216 (tpp) REVERT: B 448 LYS cc_start: 0.9337 (mmtp) cc_final: 0.9085 (tppt) REVERT: C 92 MET cc_start: 0.9628 (tpp) cc_final: 0.9285 (tpp) REVERT: C 299 ASP cc_start: 0.9124 (t0) cc_final: 0.8812 (t0) REVERT: C 448 LYS cc_start: 0.9473 (mttt) cc_final: 0.9120 (tppp) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.2079 time to fit residues: 15.1424 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 9 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.034558 restraints weight = 44999.956| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 4.40 r_work: 0.2414 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10491 Z= 0.123 Angle : 0.522 9.592 14301 Z= 0.260 Chirality : 0.042 0.198 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.102 51.092 1671 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.09 % Allowed : 8.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1329 helix: 2.30 (0.26), residues: 456 sheet: 0.26 (0.32), residues: 261 loop : -0.38 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.003 0.001 HIS C 130 PHE 0.010 0.001 PHE A 105 TYR 0.011 0.001 TYR A 345 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 6) link_NAG-ASN : angle 3.36952 ( 18) link_BETA1-4 : bond 0.01072 ( 6) link_BETA1-4 : angle 2.48392 ( 18) hydrogen bonds : bond 0.03056 ( 459) hydrogen bonds : angle 4.15660 ( 1287) SS BOND : bond 0.00129 ( 15) SS BOND : angle 0.61866 ( 30) covalent geometry : bond 0.00281 (10464) covalent geometry : angle 0.50027 (14235) ********************** 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 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9564 (tpp) cc_final: 0.9094 (tpp) REVERT: A 110 MET cc_start: 0.9517 (tpt) cc_final: 0.9139 (tpt) REVERT: A 451 ILE cc_start: 0.9343 (tt) cc_final: 0.9050 (pt) REVERT: A 454 GLN cc_start: 0.9004 (mt0) cc_final: 0.8586 (mt0) REVERT: B 92 MET cc_start: 0.9587 (tpp) cc_final: 0.9215 (tpp) REVERT: B 448 LYS cc_start: 0.9332 (mmtp) cc_final: 0.8840 (tppt) REVERT: C 92 MET cc_start: 0.9637 (tpp) cc_final: 0.9295 (tpp) REVERT: C 299 ASP cc_start: 0.9119 (t0) cc_final: 0.8806 (t0) REVERT: C 448 LYS cc_start: 0.9470 (mttt) cc_final: 0.9023 (tppp) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.2065 time to fit residues: 14.3737 Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 41 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 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 = 0.2889 r_free = 0.2889 target = 0.046655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.035796 restraints weight = 44623.703| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 4.38 r_work: 0.2435 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10491 Z= 0.090 Angle : 0.499 8.975 14301 Z= 0.250 Chirality : 0.042 0.195 1776 Planarity : 0.003 0.031 1812 Dihedral : 4.968 51.853 1671 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.17 % Allowed : 8.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1329 helix: 2.35 (0.26), residues: 456 sheet: 0.32 (0.32), residues: 261 loop : -0.38 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.001 0.000 HIS B 130 PHE 0.012 0.001 PHE A 105 TYR 0.010 0.001 TYR A 345 ARG 0.002 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 6) link_NAG-ASN : angle 3.33353 ( 18) link_BETA1-4 : bond 0.01037 ( 6) link_BETA1-4 : angle 2.47575 ( 18) hydrogen bonds : bond 0.02784 ( 459) hydrogen bonds : angle 4.09065 ( 1287) SS BOND : bond 0.00072 ( 15) SS BOND : angle 0.54714 ( 30) covalent geometry : bond 0.00200 (10464) covalent geometry : angle 0.47694 (14235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4922.20 seconds wall clock time: 88 minutes 43.40 seconds (5323.40 seconds total)