Starting phenix.real_space_refine on Wed Feb 14 21:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_29299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_29299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_29299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_29299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmx_29299/02_2024/8fmx_29299.pdb" } 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 Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.28, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.77 Conformation dependent library (CDL) restraints added in 2.1 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: 1.41 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: 3.54 Time building geometry restraints manager: 5.05 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: 100.16 - 106.92: 249 106.92 - 113.69: 6054 113.69 - 120.45: 3897 120.45 - 127.21: 3989 127.21 - 133.98: 46 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 2.440 nonbonded pdb=" O THR C 315 " pdb=" OG1 THR C 316 " model vdw 2.431 2.440 nonbonded pdb=" O THR B 315 " pdb=" OG1 THR B 316 " model vdw 2.436 2.440 nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.499 2.440 nonbonded pdb=" N ASP A 436 " pdb=" OD1 ASP A 436 " model vdw 2.500 2.520 ... (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 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: 1.040 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: 4.140 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- 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 10464 Z= 0.322 Angle : 0.930 7.599 14235 Z= 0.549 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.211 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: 0.3073 time to fit residues: 37.5220 Evaluate side-chains 44 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10464 Z= 0.309 Angle : 0.657 8.110 14235 Z= 0.343 Chirality : 0.047 0.356 1776 Planarity : 0.004 0.052 1812 Dihedral : 10.413 78.220 1671 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.78 % Allowed : 3.99 % Favored : 95.23 % 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: 0.23 (0.22), residues: 1329 helix: 1.12 (0.24), residues: 456 sheet: 0.36 (0.33), residues: 258 loop : -0.62 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.004 0.001 HIS B 130 PHE 0.016 0.002 PHE C 105 TYR 0.014 0.002 TYR A 41 ARG 0.005 0.001 ARG B 232 *********************** 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 60 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.281 Fit side-chains REVERT: A 454 GLN cc_start: 0.8802 (mt0) cc_final: 0.8591 (mt0) REVERT: C 92 MET cc_start: 0.9296 (tpp) cc_final: 0.8912 (tpp) REVERT: C 448 LYS cc_start: 0.9279 (mttt) cc_final: 0.8997 (tppp) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.2027 time to fit residues: 17.8030 Evaluate side-chains 46 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 245 SER 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 66 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN B 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10464 Z= 0.323 Angle : 0.608 7.155 14235 Z= 0.311 Chirality : 0.045 0.244 1776 Planarity : 0.003 0.037 1812 Dihedral : 7.754 54.706 1671 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.56 % Allowed : 5.38 % Favored : 93.06 % 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: 0.45 (0.23), residues: 1329 helix: 1.56 (0.25), residues: 456 sheet: 0.29 (0.33), residues: 258 loop : -0.63 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 303 HIS 0.005 0.002 HIS A 130 PHE 0.012 0.002 PHE B 277 TYR 0.011 0.001 TYR A 433 ARG 0.004 0.001 ARG B 232 *********************** 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 62 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8695 (mt0) cc_final: 0.8466 (mt0) REVERT: B 92 MET cc_start: 0.9276 (tpp) cc_final: 0.8955 (tpp) REVERT: B 110 MET cc_start: 0.8180 (tpp) cc_final: 0.7919 (tpp) REVERT: C 92 MET cc_start: 0.9284 (tpp) cc_final: 0.8913 (tpp) REVERT: C 110 MET cc_start: 0.8083 (tpp) cc_final: 0.7780 (tpt) REVERT: C 448 LYS cc_start: 0.9240 (mttt) cc_final: 0.8979 (tppp) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 0.2023 time to fit residues: 17.9435 Evaluate side-chains 49 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 367 TYR 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 118 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10464 Z= 0.155 Angle : 0.499 6.497 14235 Z= 0.261 Chirality : 0.043 0.230 1776 Planarity : 0.003 0.034 1812 Dihedral : 6.326 58.996 1671 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.13 % Allowed : 5.99 % Favored : 92.88 % 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: 0.81 (0.24), residues: 1329 helix: 1.99 (0.26), residues: 456 sheet: 0.33 (0.33), residues: 258 loop : -0.45 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 303 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE A 277 TYR 0.008 0.001 TYR B 243 ARG 0.003 0.000 ARG B 232 *********************** 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 56 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8701 (p) REVERT: A 454 GLN cc_start: 0.8734 (mt0) cc_final: 0.8521 (mt0) REVERT: B 31 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 92 MET cc_start: 0.9281 (tpp) cc_final: 0.9013 (tpp) REVERT: C 31 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8771 (p) REVERT: C 92 MET cc_start: 0.9245 (tpp) cc_final: 0.8973 (tpp) REVERT: C 110 MET cc_start: 0.8057 (tpp) cc_final: 0.7712 (tpt) REVERT: C 448 LYS cc_start: 0.9241 (mttt) cc_final: 0.8956 (tppp) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.2015 time to fit residues: 17.4774 Evaluate side-chains 48 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 306 LEU 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 72 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN C 381 ASN C 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 10464 Z= 0.506 Angle : 0.698 7.749 14235 Z= 0.344 Chirality : 0.046 0.277 1776 Planarity : 0.004 0.035 1812 Dihedral : 6.455 58.465 1671 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.56 % Allowed : 6.77 % 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: 0.52 (0.23), residues: 1329 helix: 1.81 (0.25), residues: 456 sheet: 0.10 (0.32), residues: 261 loop : -0.64 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 303 HIS 0.007 0.002 HIS A 130 PHE 0.011 0.002 PHE B 234 TYR 0.011 0.002 TYR B 39 ARG 0.006 0.001 ARG C 64 *********************** 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 58 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8850 (p) REVERT: A 92 MET cc_start: 0.9192 (tpp) cc_final: 0.8696 (tpp) REVERT: B 110 MET cc_start: 0.8081 (tpp) cc_final: 0.7772 (tpp) REVERT: B 448 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8901 (tppt) REVERT: C 31 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 92 MET cc_start: 0.9302 (tpp) cc_final: 0.8946 (tpp) REVERT: C 448 LYS cc_start: 0.9221 (mttt) cc_final: 0.8898 (tppp) outliers start: 18 outliers final: 11 residues processed: 55 average time/residue: 0.1931 time to fit residues: 17.3794 Evaluate side-chains 52 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 65 ASN 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 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10464 Z= 0.183 Angle : 0.518 9.665 14235 Z= 0.268 Chirality : 0.043 0.217 1776 Planarity : 0.003 0.032 1812 Dihedral : 6.051 55.550 1671 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.95 % Allowed : 7.29 % 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: 0.79 (0.24), residues: 1329 helix: 2.05 (0.26), residues: 456 sheet: 0.17 (0.32), residues: 261 loop : -0.46 (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 0.010 0.001 PHE B 277 TYR 0.007 0.001 TYR C 270 ARG 0.002 0.000 ARG B 232 *********************** 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 53 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8713 (p) REVERT: A 92 MET cc_start: 0.9074 (tpp) cc_final: 0.8724 (tpp) REVERT: B 31 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8840 (p) REVERT: B 92 MET cc_start: 0.9256 (tpp) cc_final: 0.8954 (tpp) REVERT: B 448 LYS cc_start: 0.9217 (mmtp) cc_final: 0.8933 (tppt) REVERT: C 31 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8787 (p) REVERT: C 92 MET cc_start: 0.9249 (tpp) cc_final: 0.8964 (tpp) REVERT: C 110 MET cc_start: 0.8063 (tpp) cc_final: 0.7810 (tpt) REVERT: C 343 MET cc_start: 0.7784 (mpp) cc_final: 0.7396 (ptp) REVERT: C 448 LYS cc_start: 0.9233 (mttt) cc_final: 0.8897 (tppp) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.2013 time to fit residues: 16.9814 Evaluate side-chains 46 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.0050 chunk 71 optimal weight: 0.0770 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10464 Z= 0.127 Angle : 0.496 8.586 14235 Z= 0.257 Chirality : 0.042 0.205 1776 Planarity : 0.003 0.035 1812 Dihedral : 5.670 51.663 1671 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.87 % Allowed : 7.90 % Favored : 91.23 % 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: 0.93 (0.24), residues: 1329 helix: 2.17 (0.26), residues: 456 sheet: 0.25 (0.32), residues: 261 loop : -0.37 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.001 0.000 HIS B 130 PHE 0.012 0.001 PHE A 105 TYR 0.006 0.001 TYR C 249 ARG 0.002 0.000 ARG C 232 *********************** 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 55 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8642 (p) REVERT: A 92 MET cc_start: 0.9017 (tpp) cc_final: 0.8751 (tpp) REVERT: A 453 ASN cc_start: 0.8905 (m-40) cc_final: 0.8700 (m110) REVERT: B 31 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 92 MET cc_start: 0.9251 (tpp) cc_final: 0.8963 (tpp) REVERT: B 448 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8872 (tppt) REVERT: C 31 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8740 (p) REVERT: C 92 MET cc_start: 0.9229 (tpp) cc_final: 0.8983 (tpp) REVERT: C 110 MET cc_start: 0.8045 (tpp) cc_final: 0.7766 (tpt) REVERT: C 448 LYS cc_start: 0.9212 (mttt) cc_final: 0.8874 (tppp) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.1885 time to fit residues: 16.3540 Evaluate side-chains 49 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10464 Z= 0.323 Angle : 0.573 7.040 14235 Z= 0.289 Chirality : 0.043 0.205 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.692 49.753 1671 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 7.90 % Favored : 91.06 % 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: 0.78 (0.24), residues: 1329 helix: 2.08 (0.26), residues: 456 sheet: 0.19 (0.32), residues: 261 loop : -0.51 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.005 0.001 HIS A 130 PHE 0.009 0.001 PHE B 234 TYR 0.009 0.001 TYR C 249 ARG 0.003 0.001 ARG C 64 *********************** 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 53 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 92 MET cc_start: 0.9152 (tpp) cc_final: 0.8796 (tpp) REVERT: A 453 ASN cc_start: 0.8917 (m-40) cc_final: 0.8706 (m110) REVERT: B 31 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 92 MET cc_start: 0.9272 (tpp) cc_final: 0.8955 (tpp) REVERT: B 448 LYS cc_start: 0.9197 (mmtp) cc_final: 0.8925 (tppt) REVERT: C 31 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 92 MET cc_start: 0.9295 (tpp) cc_final: 0.8973 (tpp) REVERT: C 110 MET cc_start: 0.8081 (tpp) cc_final: 0.7822 (tpt) REVERT: C 448 LYS cc_start: 0.9206 (mttt) cc_final: 0.8937 (tppp) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.2038 time to fit residues: 16.5348 Evaluate side-chains 51 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 343 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10464 Z= 0.138 Angle : 0.490 7.719 14235 Z= 0.254 Chirality : 0.042 0.196 1776 Planarity : 0.003 0.032 1812 Dihedral : 5.478 51.352 1671 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.04 % Allowed : 8.25 % 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 (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: 0.97 (0.24), residues: 1329 helix: 2.20 (0.26), residues: 456 sheet: 0.30 (0.32), residues: 261 loop : -0.38 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 303 HIS 0.002 0.000 HIS A 130 PHE 0.010 0.001 PHE A 105 TYR 0.007 0.001 TYR B 270 ARG 0.002 0.000 ARG A 104 *********************** 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 52 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 92 MET cc_start: 0.9035 (tpp) cc_final: 0.8754 (tpp) REVERT: A 453 ASN cc_start: 0.8881 (m-40) cc_final: 0.8647 (m110) REVERT: B 31 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8731 (p) REVERT: B 92 MET cc_start: 0.9269 (tpp) cc_final: 0.8995 (tpp) REVERT: B 448 LYS cc_start: 0.9214 (mmtp) cc_final: 0.8947 (tppt) REVERT: C 31 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8663 (p) REVERT: C 92 MET cc_start: 0.9231 (tpp) cc_final: 0.8974 (tpp) REVERT: C 110 MET cc_start: 0.8001 (tpp) cc_final: 0.7769 (tpt) REVERT: C 448 LYS cc_start: 0.9241 (mttt) cc_final: 0.8986 (tppp) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.1984 time to fit residues: 15.9357 Evaluate side-chains 49 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 343 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10464 Z= 0.225 Angle : 0.514 7.972 14235 Z= 0.263 Chirality : 0.042 0.192 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.415 50.592 1671 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.95 % Allowed : 8.33 % 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 (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: 0.94 (0.24), residues: 1329 helix: 2.23 (0.26), residues: 456 sheet: 0.29 (0.32), residues: 261 loop : -0.44 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 303 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE A 105 TYR 0.008 0.001 TYR C 249 ARG 0.002 0.000 ARG B 232 ********************** 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 51 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 92 MET cc_start: 0.9075 (tpp) cc_final: 0.8765 (tpp) REVERT: A 453 ASN cc_start: 0.8886 (m-40) cc_final: 0.8651 (m110) REVERT: B 31 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 92 MET cc_start: 0.9292 (tpp) cc_final: 0.8988 (tpp) REVERT: B 448 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8948 (tppt) REVERT: C 31 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8696 (p) REVERT: C 92 MET cc_start: 0.9277 (tpp) cc_final: 0.9005 (tpp) REVERT: C 110 MET cc_start: 0.8048 (tpp) cc_final: 0.7825 (tpt) REVERT: C 448 LYS cc_start: 0.9189 (mttt) cc_final: 0.8944 (tppp) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.2036 time to fit residues: 15.8733 Evaluate side-chains 50 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 343 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.035199 restraints weight = 44225.279| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 4.36 r_work: 0.2422 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10464 Z= 0.165 Angle : 0.483 6.881 14235 Z= 0.251 Chirality : 0.042 0.186 1776 Planarity : 0.003 0.031 1812 Dihedral : 5.274 51.211 1671 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.87 % Allowed : 8.42 % 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 (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: 0.99 (0.24), residues: 1329 helix: 2.27 (0.26), residues: 456 sheet: 0.30 (0.32), residues: 261 loop : -0.40 (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 0.006 0.001 TYR C 270 ARG 0.001 0.000 ARG C 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.24 seconds wall clock time: 35 minutes 48.89 seconds (2148.89 seconds total)