Starting phenix.real_space_refine on Sat Feb 17 21:41:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/02_2024/8hgs_34746.pdb" } resolution = 3.81 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9900 atoms to isotropic. 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 126 5.16 5 C 6228 2.51 5 N 1768 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 494": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.77, per 1000 atoms: 0.57 Number of scatterers: 10080 At special positions: 0 Unit cell: (75.97, 129.47, 130.54, 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 126 16.00 O 1958 8.00 N 1768 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 499 " distance=2.04 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 539 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 617 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-3 " NAG E 2 " - " BMA E 3 " " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG B 801 " - " ASN B 56 " " NAG B 802 " - " ASN B 175 " " NAG E 1 " - " ASN A 352 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 13.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.537A pdb=" N LYS A 80 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.638A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.823A pdb=" N CYS A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.805A pdb=" N CYS A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.521A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.712A pdb=" N LYS A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 4.203A pdb=" N PHE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.087A pdb=" N THR A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 removed outlier: 3.690A pdb=" N GLY A 434 " --> pdb=" O LYS A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.051A pdb=" N ALA A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.785A pdb=" N CYS A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.564A pdb=" N HIS C 10 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 11 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.565A pdb=" N HIS D 10 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 11 " --> pdb=" O LEU D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 11' Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.537A pdb=" N LYS B 80 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 81 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.639A pdb=" N GLY B 197 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 198 " --> pdb=" O PRO B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 198' Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.823A pdb=" N CYS B 207 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.804A pdb=" N CYS B 248 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.520A pdb=" N PHE B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.712A pdb=" N LYS B 357 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.203A pdb=" N PHE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 4.087A pdb=" N THR B 397 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 removed outlier: 3.690A pdb=" N GLY B 434 " --> pdb=" O LYS B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 476 through 481 removed outlier: 4.039A pdb=" N LEU B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 4.051A pdb=" N ALA B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.785A pdb=" N CYS B 579 " --> pdb=" O PRO B 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS A 31 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 64 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 33 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU A 66 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 107 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS A 31 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 64 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 33 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU A 66 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N LEU A 90 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN A 94 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 69 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.640A pdb=" N GLN A 276 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.986A pdb=" N CYS A 337 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 369 through 371 removed outlier: 3.724A pdb=" N LEU A 406 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB4, first strand: chain 'A' and resid 548 through 551 Processing sheet with id=AB5, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AB6, first strand: chain 'A' and resid 597 through 599 removed outlier: 5.309A pdb=" N VAL A 607 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.539A pdb=" N CYS D 33 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AC1, first strand: chain 'B' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS B 31 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 64 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY B 33 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 66 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 107 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS B 31 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 64 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY B 33 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 66 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N LEU B 90 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 65 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA B 92 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 67 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN B 94 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR B 69 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 89 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 122 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 91 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 119 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER B 151 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 121 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 256 Processing sheet with id=AC4, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.640A pdb=" N GLN B 276 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AC6, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AC7, first strand: chain 'B' and resid 315 through 317 Processing sheet with id=AC8, first strand: chain 'B' and resid 337 through 338 removed outlier: 6.985A pdb=" N CYS B 337 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 369 through 371 removed outlier: 3.724A pdb=" N LEU B 406 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE B 462 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 439 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AD2, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AD3, first strand: chain 'B' and resid 548 through 551 Processing sheet with id=AD4, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AD5, first strand: chain 'B' and resid 597 through 599 removed outlier: 5.308A pdb=" N VAL B 607 " --> pdb=" O GLY B 598 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 252 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: 2.81 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3386 1.35 - 1.47: 2225 1.47 - 1.59: 4515 1.59 - 1.71: 2 1.71 - 1.83: 148 Bond restraints: 10276 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.591 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.98: 338 106.98 - 113.75: 5622 113.75 - 120.53: 3787 120.53 - 127.30: 4047 127.30 - 134.08: 102 Bond angle restraints: 13896 Sorted by residual: angle pdb=" N ALA A 258 " pdb=" CA ALA A 258 " pdb=" C ALA A 258 " ideal model delta sigma weight residual 114.64 108.32 6.32 1.52e+00 4.33e-01 1.73e+01 angle pdb=" N ALA B 258 " pdb=" CA ALA B 258 " pdb=" C ALA B 258 " ideal model delta sigma weight residual 114.64 108.33 6.31 1.52e+00 4.33e-01 1.72e+01 angle pdb=" C CYS B 470 " pdb=" N TYR B 471 " pdb=" CA TYR B 471 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C CYS A 470 " pdb=" N TYR A 471 " pdb=" CA TYR A 471 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N TYR A 471 " pdb=" CA TYR A 471 " pdb=" C TYR A 471 " ideal model delta sigma weight residual 110.80 118.50 -7.70 2.13e+00 2.20e-01 1.31e+01 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 6264 21.18 - 42.35: 170 42.35 - 63.53: 48 63.53 - 84.71: 26 84.71 - 105.88: 28 Dihedral angle restraints: 6536 sinusoidal: 2860 harmonic: 3676 Sorted by residual: dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 20 " pdb=" CB CYS D 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C 6 " pdb=" SG CYS C 6 " pdb=" SG CYS C 20 " pdb=" CB CYS C 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.02 -57.02 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -137.77 51.77 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 6533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1365 0.087 - 0.174: 175 0.174 - 0.261: 5 0.261 - 0.348: 3 0.348 - 0.436: 2 Chirality restraints: 1550 Sorted by residual: chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1547 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 256 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C ASP B 256 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 256 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ASP A 256 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 511 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO B 512 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.032 5.00e-02 4.00e+02 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3241 2.87 - 3.38: 8786 3.38 - 3.89: 16257 3.89 - 4.39: 17676 4.39 - 4.90: 30946 Nonbonded interactions: 76906 Sorted by model distance: nonbonded pdb=" OH TYR D 22 " pdb=" OD1 ASP D 27 " model vdw 2.368 2.440 nonbonded pdb=" OH TYR C 22 " pdb=" OD1 ASP C 27 " model vdw 2.368 2.440 nonbonded pdb=" OG1 THR A 302 " pdb=" OG SER A 306 " model vdw 2.379 2.440 nonbonded pdb=" O ARG B 309 " pdb=" NH1 ARG B 429 " model vdw 2.379 2.520 nonbonded pdb=" OG1 THR B 302 " pdb=" OG SER B 306 " model vdw 2.380 2.440 ... (remaining 76901 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 11.870 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 28.470 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 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 : 0.004 0.068 10276 Z= 0.262 Angle : 0.748 9.519 13896 Z= 0.396 Chirality : 0.057 0.436 1550 Planarity : 0.006 0.058 1814 Dihedral : 13.676 105.883 4020 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -3.50 (0.19), residues: 1272 helix: -3.75 (0.39), residues: 40 sheet: -3.30 (0.36), residues: 120 loop : -2.40 (0.15), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 50 HIS 0.006 0.001 HIS A 47 PHE 0.021 0.002 PHE A 404 TYR 0.013 0.001 TYR A 88 ARG 0.003 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7746 (mm110) cc_final: 0.7430 (mm-40) REVERT: A 46 ASP cc_start: 0.7171 (m-30) cc_final: 0.6741 (m-30) REVERT: A 59 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 64 ASN cc_start: 0.7707 (m-40) cc_final: 0.7225 (m-40) REVERT: A 88 TYR cc_start: 0.7328 (p90) cc_final: 0.7007 (p90) REVERT: A 93 LEU cc_start: 0.8191 (mt) cc_final: 0.7938 (mt) REVERT: A 105 GLN cc_start: 0.7984 (mt0) cc_final: 0.7562 (mt0) REVERT: A 126 ASP cc_start: 0.6266 (p0) cc_final: 0.5447 (p0) REVERT: A 130 THR cc_start: 0.6847 (p) cc_final: 0.6044 (p) REVERT: A 137 MET cc_start: 0.7581 (mtm) cc_final: 0.7354 (mtp) REVERT: A 139 ASN cc_start: 0.8003 (m-40) cc_final: 0.7336 (m-40) REVERT: A 149 ARG cc_start: 0.6535 (ttt90) cc_final: 0.6286 (ttt-90) REVERT: A 249 LEU cc_start: 0.7802 (mt) cc_final: 0.7517 (mt) REVERT: A 269 LEU cc_start: 0.6388 (mt) cc_final: 0.6102 (tp) REVERT: A 275 TYR cc_start: 0.8322 (m-80) cc_final: 0.8021 (m-80) REVERT: A 300 VAL cc_start: 0.8228 (t) cc_final: 0.8017 (t) REVERT: A 318 MET cc_start: 0.3937 (pp-130) cc_final: 0.3605 (pp-130) REVERT: A 399 LYS cc_start: 0.6567 (mtpp) cc_final: 0.6308 (mtpp) REVERT: A 422 ASN cc_start: 0.7591 (m-40) cc_final: 0.7137 (m-40) REVERT: A 452 SER cc_start: 0.6756 (p) cc_final: 0.6447 (t) REVERT: A 458 ASP cc_start: 0.7178 (t0) cc_final: 0.6800 (t0) REVERT: A 462 ILE cc_start: 0.6221 (tt) cc_final: 0.5917 (tt) REVERT: A 541 LEU cc_start: 0.6522 (mt) cc_final: 0.6226 (mp) REVERT: A 618 HIS cc_start: 0.6176 (m-70) cc_final: 0.5735 (m90) REVERT: C 21 MET cc_start: 0.7008 (ptt) cc_final: 0.6602 (ptt) REVERT: D 21 MET cc_start: 0.6977 (ptt) cc_final: 0.6640 (ptt) REVERT: D 40 GLU cc_start: 0.7091 (tt0) cc_final: 0.6812 (tt0) REVERT: B 37 LYS cc_start: 0.7443 (mttm) cc_final: 0.6922 (ttmt) REVERT: B 40 GLN cc_start: 0.7040 (tt0) cc_final: 0.6720 (tt0) REVERT: B 59 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 80 LYS cc_start: 0.8240 (mttt) cc_final: 0.7707 (mttt) REVERT: B 88 TYR cc_start: 0.7747 (p90) cc_final: 0.7510 (p90) REVERT: B 105 GLN cc_start: 0.7888 (mt0) cc_final: 0.7588 (mt0) REVERT: B 126 ASP cc_start: 0.6111 (p0) cc_final: 0.5486 (p0) REVERT: B 144 LEU cc_start: 0.8020 (mm) cc_final: 0.7809 (mp) REVERT: B 149 ARG cc_start: 0.6679 (ttt90) cc_final: 0.6327 (ttt90) REVERT: B 171 ASP cc_start: 0.7103 (t0) cc_final: 0.6698 (t0) REVERT: B 249 LEU cc_start: 0.7435 (mt) cc_final: 0.7232 (mt) REVERT: B 309 ARG cc_start: 0.6379 (mtt180) cc_final: 0.5865 (mtt-85) REVERT: B 318 MET cc_start: 0.4580 (pp-130) cc_final: 0.4113 (pp-130) REVERT: B 321 ASP cc_start: 0.5945 (m-30) cc_final: 0.5620 (m-30) REVERT: B 325 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7781 (mmtm) REVERT: B 345 PHE cc_start: 0.6638 (m-10) cc_final: 0.6354 (m-10) REVERT: B 360 LYS cc_start: 0.7949 (tppp) cc_final: 0.7713 (tppp) REVERT: B 369 LEU cc_start: 0.7280 (mt) cc_final: 0.7063 (mt) REVERT: B 399 LYS cc_start: 0.6562 (mtpp) cc_final: 0.6076 (mtpp) REVERT: B 400 GLU cc_start: 0.6942 (tt0) cc_final: 0.6672 (tt0) REVERT: B 427 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7726 (mmt90) REVERT: B 436 PHE cc_start: 0.5974 (m-80) cc_final: 0.5756 (m-80) REVERT: B 454 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7394 (mmtt) REVERT: B 458 ASP cc_start: 0.7467 (t0) cc_final: 0.6731 (t0) REVERT: B 460 ASP cc_start: 0.6374 (m-30) cc_final: 0.5770 (m-30) REVERT: B 471 TYR cc_start: 0.3317 (m-80) cc_final: 0.2441 (m-80) REVERT: B 475 ILE cc_start: 0.6263 (mm) cc_final: 0.6045 (mp) REVERT: B 521 ARG cc_start: 0.6689 (ppt-90) cc_final: 0.6430 (ppt-90) REVERT: B 551 GLU cc_start: 0.7578 (pt0) cc_final: 0.7152 (pt0) REVERT: B 557 GLN cc_start: 0.7171 (mt0) cc_final: 0.6690 (mt0) REVERT: B 600 MET cc_start: 0.6807 (tpp) cc_final: 0.6461 (tpp) REVERT: B 618 HIS cc_start: 0.6680 (m-70) cc_final: 0.6262 (m-70) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2803 time to fit residues: 118.5147 Evaluate side-chains 268 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 52 GLN A 94 ASN A 139 ASN A 206 ASN A 338 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 468 ASN A 552 ASN A 559 HIS C 10 HIS D 10 HIS D 16 HIS B 47 HIS ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 432 GLN B 433 HIS B 444 ASN B 468 ASN B 559 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 10276 Z= 0.400 Angle : 0.822 15.831 13896 Z= 0.412 Chirality : 0.056 0.316 1550 Planarity : 0.005 0.070 1814 Dihedral : 12.814 80.071 1620 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.96 % Allowed : 8.57 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.52 (0.21), residues: 1272 helix: -0.75 (0.90), residues: 42 sheet: -2.44 (0.46), residues: 88 loop : -1.84 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 410 HIS 0.009 0.002 HIS B 433 PHE 0.022 0.003 PHE B 180 TYR 0.021 0.002 TYR A 113 ARG 0.011 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7973 (mttt) cc_final: 0.7747 (mttp) REVERT: A 46 ASP cc_start: 0.7461 (m-30) cc_final: 0.6909 (m-30) REVERT: A 58 CYS cc_start: 0.5200 (t) cc_final: 0.4835 (t) REVERT: A 59 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 80 LYS cc_start: 0.8110 (mttt) cc_final: 0.7541 (mtmt) REVERT: A 83 GLN cc_start: 0.7521 (mt0) cc_final: 0.6761 (mt0) REVERT: A 88 TYR cc_start: 0.7440 (p90) cc_final: 0.7090 (p90) REVERT: A 105 GLN cc_start: 0.8049 (mt0) cc_final: 0.7739 (mt0) REVERT: A 108 ARG cc_start: 0.7510 (mtt-85) cc_final: 0.6800 (mmm-85) REVERT: A 111 MET cc_start: 0.7439 (ptm) cc_final: 0.7186 (ptm) REVERT: A 112 TYR cc_start: 0.7605 (m-80) cc_final: 0.6163 (m-80) REVERT: A 124 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: A 125 TYR cc_start: 0.7665 (p90) cc_final: 0.7335 (p90) REVERT: A 139 ASN cc_start: 0.8177 (m110) cc_final: 0.7814 (m-40) REVERT: A 149 ARG cc_start: 0.6946 (ttt90) cc_final: 0.6542 (ttt-90) REVERT: A 178 MET cc_start: 0.7517 (mmm) cc_final: 0.7305 (mmp) REVERT: A 253 LYS cc_start: 0.8200 (mttp) cc_final: 0.7823 (mttp) REVERT: A 299 TYR cc_start: 0.7910 (m-80) cc_final: 0.7478 (m-80) REVERT: A 340 ILE cc_start: 0.8083 (mp) cc_final: 0.7694 (mt) REVERT: A 350 SER cc_start: 0.6971 (t) cc_final: 0.6611 (p) REVERT: A 357 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7703 (mtmm) REVERT: A 399 LYS cc_start: 0.6930 (mtpp) cc_final: 0.6455 (mtpp) REVERT: A 405 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6777 (tp) REVERT: A 426 ILE cc_start: 0.7673 (mt) cc_final: 0.7078 (tt) REVERT: A 436 PHE cc_start: 0.7152 (m-80) cc_final: 0.6913 (m-80) REVERT: A 548 GLU cc_start: 0.5348 (mp0) cc_final: 0.4902 (mp0) REVERT: A 559 HIS cc_start: 0.6838 (t-90) cc_final: 0.6557 (t-90) REVERT: A 618 HIS cc_start: 0.6845 (m-70) cc_final: 0.6402 (m-70) REVERT: B 32 GLN cc_start: 0.7977 (mm110) cc_final: 0.7603 (mt0) REVERT: B 48 PHE cc_start: 0.7982 (t80) cc_final: 0.7541 (t80) REVERT: B 59 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6904 (mt-10) REVERT: B 80 LYS cc_start: 0.8288 (mttt) cc_final: 0.7803 (mttt) REVERT: B 88 TYR cc_start: 0.7605 (p90) cc_final: 0.7282 (p90) REVERT: B 149 ARG cc_start: 0.7125 (ttt90) cc_final: 0.6867 (ttt90) REVERT: B 171 ASP cc_start: 0.7262 (t0) cc_final: 0.6836 (t0) REVERT: B 209 LYS cc_start: 0.7949 (ptpp) cc_final: 0.7580 (mtmm) REVERT: B 253 LYS cc_start: 0.8222 (mttp) cc_final: 0.7866 (mttp) REVERT: B 278 ASP cc_start: 0.7134 (m-30) cc_final: 0.6665 (m-30) REVERT: B 321 ASP cc_start: 0.6336 (m-30) cc_final: 0.5789 (m-30) REVERT: B 325 LYS cc_start: 0.8266 (mmtp) cc_final: 0.8010 (mmtp) REVERT: B 345 PHE cc_start: 0.7520 (m-10) cc_final: 0.7175 (m-10) REVERT: B 361 ASN cc_start: 0.7134 (m-40) cc_final: 0.6847 (t0) REVERT: B 364 SER cc_start: 0.8705 (p) cc_final: 0.8435 (m) REVERT: B 369 LEU cc_start: 0.8024 (mt) cc_final: 0.7685 (mt) REVERT: B 399 LYS cc_start: 0.6823 (mtpp) cc_final: 0.6218 (mtpp) REVERT: B 400 GLU cc_start: 0.7200 (tt0) cc_final: 0.6927 (tt0) REVERT: B 427 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7757 (mmt90) REVERT: B 451 ARG cc_start: 0.7368 (ptp90) cc_final: 0.6156 (ptp90) REVERT: B 454 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7503 (mmtt) REVERT: B 458 ASP cc_start: 0.7786 (t0) cc_final: 0.7037 (t0) REVERT: B 487 LYS cc_start: 0.7476 (pttp) cc_final: 0.7134 (pttp) REVERT: B 521 ARG cc_start: 0.7034 (ppt-90) cc_final: 0.6731 (ppt-90) REVERT: B 618 HIS cc_start: 0.6896 (m-70) cc_final: 0.6455 (m90) outliers start: 22 outliers final: 10 residues processed: 322 average time/residue: 0.2850 time to fit residues: 118.7810 Evaluate side-chains 297 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 285 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 31 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.0570 chunk 113 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 52 GLN A 235 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 433 HIS A 493 ASN A 504 GLN C 10 HIS C 16 HIS D 10 HIS B 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10276 Z= 0.233 Angle : 0.689 9.790 13896 Z= 0.342 Chirality : 0.052 0.339 1550 Planarity : 0.004 0.050 1814 Dihedral : 10.229 65.687 1620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.21 % Favored : 93.55 % Rotamer: Outliers : 1.88 % Allowed : 11.70 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.24 (0.22), residues: 1272 helix: -0.58 (0.92), residues: 40 sheet: -2.43 (0.55), residues: 64 loop : -1.64 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 49 HIS 0.003 0.001 HIS B 47 PHE 0.021 0.002 PHE B 48 TYR 0.011 0.001 TYR D 37 ARG 0.006 0.001 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 298 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8113 (mm110) cc_final: 0.7868 (mp10) REVERT: A 37 LYS cc_start: 0.7786 (mttt) cc_final: 0.7564 (mttm) REVERT: A 46 ASP cc_start: 0.7283 (m-30) cc_final: 0.6794 (m-30) REVERT: A 58 CYS cc_start: 0.5313 (t) cc_final: 0.4969 (t) REVERT: A 59 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 64 ASN cc_start: 0.8194 (m-40) cc_final: 0.7629 (m-40) REVERT: A 80 LYS cc_start: 0.8120 (mttt) cc_final: 0.7518 (mtmt) REVERT: A 83 GLN cc_start: 0.7547 (mt0) cc_final: 0.6790 (mt0) REVERT: A 105 GLN cc_start: 0.8041 (mt0) cc_final: 0.7816 (mt0) REVERT: A 125 TYR cc_start: 0.7573 (p90) cc_final: 0.7181 (p90) REVERT: A 137 MET cc_start: 0.7471 (mtp) cc_final: 0.7256 (mtm) REVERT: A 249 LEU cc_start: 0.7383 (mt) cc_final: 0.7179 (mt) REVERT: A 254 PHE cc_start: 0.7230 (m-10) cc_final: 0.6966 (m-80) REVERT: A 271 ASN cc_start: 0.7862 (t0) cc_final: 0.7638 (t0) REVERT: A 335 LYS cc_start: 0.7530 (tptp) cc_final: 0.7196 (tptp) REVERT: A 350 SER cc_start: 0.6887 (t) cc_final: 0.6586 (p) REVERT: A 357 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7735 (mtmm) REVERT: A 399 LYS cc_start: 0.6979 (mtpp) cc_final: 0.6509 (mtpp) REVERT: A 405 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6780 (tp) REVERT: A 426 ILE cc_start: 0.7586 (mt) cc_final: 0.6993 (tt) REVERT: A 458 ASP cc_start: 0.7558 (t0) cc_final: 0.7033 (t0) REVERT: A 561 GLU cc_start: 0.5884 (tp30) cc_final: 0.3054 (mm-30) REVERT: A 618 HIS cc_start: 0.6798 (m-70) cc_final: 0.6217 (m170) REVERT: D 44 TYR cc_start: 0.6912 (m-10) cc_final: 0.6539 (m-80) REVERT: B 59 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 80 LYS cc_start: 0.8351 (mttt) cc_final: 0.7763 (mttt) REVERT: B 88 TYR cc_start: 0.7623 (p90) cc_final: 0.7268 (p90) REVERT: B 112 TYR cc_start: 0.7843 (m-80) cc_final: 0.6513 (m-80) REVERT: B 149 ARG cc_start: 0.7080 (ttt90) cc_final: 0.6785 (ttt-90) REVERT: B 168 VAL cc_start: 0.8120 (t) cc_final: 0.7770 (p) REVERT: B 171 ASP cc_start: 0.7175 (t0) cc_final: 0.6769 (t0) REVERT: B 253 LYS cc_start: 0.7905 (mttp) cc_final: 0.7697 (mttp) REVERT: B 260 CYS cc_start: 0.5615 (OUTLIER) cc_final: 0.4406 (m) REVERT: B 278 ASP cc_start: 0.7091 (m-30) cc_final: 0.6570 (m-30) REVERT: B 286 SER cc_start: 0.6666 (m) cc_final: 0.6256 (m) REVERT: B 325 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7948 (mmtp) REVERT: B 345 PHE cc_start: 0.7532 (m-10) cc_final: 0.7259 (m-10) REVERT: B 357 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7463 (mtmm) REVERT: B 361 ASN cc_start: 0.7137 (m-40) cc_final: 0.6881 (t0) REVERT: B 364 SER cc_start: 0.8704 (p) cc_final: 0.8426 (m) REVERT: B 369 LEU cc_start: 0.8079 (mt) cc_final: 0.7768 (mt) REVERT: B 382 THR cc_start: 0.1956 (OUTLIER) cc_final: 0.1721 (m) REVERT: B 391 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7185 (mt-10) REVERT: B 399 LYS cc_start: 0.6964 (mtpp) cc_final: 0.6368 (mtpp) REVERT: B 400 GLU cc_start: 0.7179 (tt0) cc_final: 0.6769 (tt0) REVERT: B 415 THR cc_start: 0.7409 (p) cc_final: 0.7066 (t) REVERT: B 427 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7680 (mmt90) REVERT: B 451 ARG cc_start: 0.7343 (ptp90) cc_final: 0.6423 (ptp90) REVERT: B 454 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7483 (mmtt) REVERT: B 458 ASP cc_start: 0.7575 (t0) cc_final: 0.6756 (t0) REVERT: B 487 LYS cc_start: 0.7502 (pttp) cc_final: 0.7202 (pttp) REVERT: B 521 ARG cc_start: 0.7156 (ppt-90) cc_final: 0.6722 (ppt-90) REVERT: B 559 HIS cc_start: 0.6989 (t-90) cc_final: 0.6689 (t-90) REVERT: B 561 GLU cc_start: 0.6601 (tp30) cc_final: 0.6364 (tp30) REVERT: B 581 GLN cc_start: 0.7914 (tt0) cc_final: 0.7686 (tt0) REVERT: B 618 HIS cc_start: 0.6954 (m-70) cc_final: 0.6515 (m90) outliers start: 21 outliers final: 9 residues processed: 307 average time/residue: 0.3054 time to fit residues: 120.1783 Evaluate side-chains 295 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 283 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 235 GLN B 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 10276 Z= 0.383 Angle : 0.808 15.583 13896 Z= 0.402 Chirality : 0.053 0.315 1550 Planarity : 0.005 0.045 1814 Dihedral : 9.070 61.343 1620 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.65 % Favored : 91.19 % Rotamer: Outliers : 3.48 % Allowed : 12.50 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.26 (0.22), residues: 1272 helix: -1.04 (0.85), residues: 42 sheet: -2.20 (0.55), residues: 78 loop : -1.64 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 49 HIS 0.008 0.002 HIS A 370 PHE 0.029 0.003 PHE B 404 TYR 0.032 0.002 TYR B 471 ARG 0.006 0.001 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7325 (mttp) cc_final: 0.7072 (mttp) REVERT: A 46 ASP cc_start: 0.7394 (m-30) cc_final: 0.6913 (m-30) REVERT: A 58 CYS cc_start: 0.5290 (t) cc_final: 0.4858 (t) REVERT: A 59 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 64 ASN cc_start: 0.8110 (m-40) cc_final: 0.7487 (m-40) REVERT: A 79 LEU cc_start: 0.8453 (mt) cc_final: 0.8212 (mp) REVERT: A 80 LYS cc_start: 0.8301 (mttt) cc_final: 0.7591 (mttt) REVERT: A 111 MET cc_start: 0.7525 (ptm) cc_final: 0.7247 (ptm) REVERT: A 125 TYR cc_start: 0.7826 (p90) cc_final: 0.7502 (p90) REVERT: A 137 MET cc_start: 0.7444 (mtp) cc_final: 0.7136 (mtm) REVERT: A 149 ARG cc_start: 0.7134 (ttt90) cc_final: 0.6686 (ttt-90) REVERT: A 163 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7647 (tm-30) REVERT: A 168 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8201 (p) REVERT: A 235 GLN cc_start: 0.7374 (mm110) cc_final: 0.6268 (mm-40) REVERT: A 252 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7131 (ttp80) REVERT: A 253 LYS cc_start: 0.8239 (mttp) cc_final: 0.7936 (mttp) REVERT: A 256 ASP cc_start: 0.6866 (m-30) cc_final: 0.6358 (m-30) REVERT: A 299 TYR cc_start: 0.8014 (m-80) cc_final: 0.7242 (m-80) REVERT: A 335 LYS cc_start: 0.7469 (tptp) cc_final: 0.7139 (tptp) REVERT: A 350 SER cc_start: 0.7059 (t) cc_final: 0.6692 (p) REVERT: A 357 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7765 (mtmm) REVERT: A 370 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7381 (m170) REVERT: A 399 LYS cc_start: 0.7036 (mtpp) cc_final: 0.6600 (mtpp) REVERT: A 405 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6821 (tp) REVERT: A 426 ILE cc_start: 0.7661 (mt) cc_final: 0.7117 (tt) REVERT: A 446 THR cc_start: 0.7113 (m) cc_final: 0.6769 (m) REVERT: A 454 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7468 (mmtt) REVERT: A 458 ASP cc_start: 0.7684 (t0) cc_final: 0.7165 (t0) REVERT: A 460 ASP cc_start: 0.6571 (m-30) cc_final: 0.6133 (m-30) REVERT: A 548 GLU cc_start: 0.4269 (mp0) cc_final: 0.4009 (mp0) REVERT: A 618 HIS cc_start: 0.7223 (m-70) cc_final: 0.6620 (m-70) REVERT: B 32 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7540 (mt0) REVERT: B 59 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 80 LYS cc_start: 0.8464 (mttt) cc_final: 0.7849 (mttt) REVERT: B 88 TYR cc_start: 0.7373 (p90) cc_final: 0.7172 (p90) REVERT: B 112 TYR cc_start: 0.7750 (m-80) cc_final: 0.6338 (m-80) REVERT: B 134 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6674 (mm-30) REVERT: B 139 ASN cc_start: 0.7910 (m110) cc_final: 0.7684 (m-40) REVERT: B 149 ARG cc_start: 0.7258 (ttt90) cc_final: 0.7056 (ttt-90) REVERT: B 168 VAL cc_start: 0.8207 (t) cc_final: 0.7927 (p) REVERT: B 171 ASP cc_start: 0.7338 (t0) cc_final: 0.6766 (t0) REVERT: B 172 PHE cc_start: 0.8030 (m-10) cc_final: 0.7455 (m-10) REVERT: B 260 CYS cc_start: 0.5886 (OUTLIER) cc_final: 0.4870 (m) REVERT: B 278 ASP cc_start: 0.7249 (m-30) cc_final: 0.6723 (m-30) REVERT: B 285 TYR cc_start: 0.7352 (m-80) cc_final: 0.7079 (m-80) REVERT: B 286 SER cc_start: 0.6885 (m) cc_final: 0.6504 (m) REVERT: B 299 TYR cc_start: 0.8009 (m-80) cc_final: 0.7513 (m-80) REVERT: B 325 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7909 (mmtp) REVERT: B 357 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7813 (mtmm) REVERT: B 364 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 382 THR cc_start: 0.2820 (OUTLIER) cc_final: 0.2578 (m) REVERT: B 388 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7175 (p0) REVERT: B 396 LYS cc_start: 0.7791 (mttt) cc_final: 0.7171 (mttm) REVERT: B 399 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6477 (mtpp) REVERT: B 400 GLU cc_start: 0.7191 (tt0) cc_final: 0.6825 (tt0) REVERT: B 454 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7519 (mmtt) REVERT: B 458 ASP cc_start: 0.7679 (t0) cc_final: 0.6942 (t0) REVERT: B 487 LYS cc_start: 0.7656 (pttp) cc_final: 0.7270 (pttp) REVERT: B 521 ARG cc_start: 0.7371 (ppt-90) cc_final: 0.6970 (ttp-110) REVERT: B 553 SER cc_start: 0.7885 (m) cc_final: 0.7622 (t) REVERT: B 559 HIS cc_start: 0.7381 (t-90) cc_final: 0.6930 (t-90) REVERT: B 618 HIS cc_start: 0.7403 (m-70) cc_final: 0.6829 (m90) outliers start: 39 outliers final: 23 residues processed: 329 average time/residue: 0.2849 time to fit residues: 121.7324 Evaluate side-chains 337 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 307 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.3980 chunk 69 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10276 Z= 0.236 Angle : 0.678 9.774 13896 Z= 0.335 Chirality : 0.050 0.339 1550 Planarity : 0.004 0.048 1814 Dihedral : 8.133 56.283 1620 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.84 % Favored : 92.85 % Rotamer: Outliers : 2.86 % Allowed : 14.91 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.04 (0.23), residues: 1272 helix: -0.75 (0.90), residues: 40 sheet: -2.25 (0.53), residues: 82 loop : -1.46 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 49 HIS 0.004 0.001 HIS B 507 PHE 0.017 0.002 PHE B 404 TYR 0.017 0.002 TYR D 37 ARG 0.011 0.001 ARG B 533 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7319 (mttp) cc_final: 0.7065 (mttp) REVERT: A 46 ASP cc_start: 0.7325 (m-30) cc_final: 0.6874 (m-30) REVERT: A 58 CYS cc_start: 0.5313 (t) cc_final: 0.4882 (t) REVERT: A 59 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 64 ASN cc_start: 0.8199 (m-40) cc_final: 0.7545 (m-40) REVERT: A 80 LYS cc_start: 0.8270 (mttt) cc_final: 0.7589 (mttt) REVERT: A 83 GLN cc_start: 0.7500 (mt0) cc_final: 0.6648 (mt0) REVERT: A 111 MET cc_start: 0.7388 (ptm) cc_final: 0.7161 (ptm) REVERT: A 125 TYR cc_start: 0.7778 (p90) cc_final: 0.7546 (p90) REVERT: A 137 MET cc_start: 0.7385 (mtp) cc_final: 0.7121 (mtm) REVERT: A 149 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6711 (ttt-90) REVERT: A 168 VAL cc_start: 0.8485 (t) cc_final: 0.8143 (p) REVERT: A 253 LYS cc_start: 0.8289 (mttp) cc_final: 0.8055 (mttp) REVERT: A 299 TYR cc_start: 0.7972 (m-80) cc_final: 0.7207 (m-80) REVERT: A 335 LYS cc_start: 0.7463 (tptp) cc_final: 0.7207 (tptp) REVERT: A 350 SER cc_start: 0.7114 (t) cc_final: 0.6784 (p) REVERT: A 357 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7714 (mtmm) REVERT: A 399 LYS cc_start: 0.7040 (mtpp) cc_final: 0.6580 (mtpp) REVERT: A 405 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6803 (tp) REVERT: A 408 GLN cc_start: 0.7864 (mt0) cc_final: 0.7160 (tt0) REVERT: A 426 ILE cc_start: 0.7607 (mt) cc_final: 0.6998 (tt) REVERT: A 451 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6998 (ptp90) REVERT: A 454 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7476 (mmtt) REVERT: A 458 ASP cc_start: 0.7665 (t0) cc_final: 0.7087 (t0) REVERT: A 460 ASP cc_start: 0.6525 (m-30) cc_final: 0.6187 (m-30) REVERT: A 522 ASP cc_start: 0.6754 (t0) cc_final: 0.5661 (t0) REVERT: A 533 ARG cc_start: 0.7358 (tpp-160) cc_final: 0.6985 (tpp-160) REVERT: A 548 GLU cc_start: 0.3965 (mp0) cc_final: 0.3579 (mp0) REVERT: A 586 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7046 (tp) REVERT: A 618 HIS cc_start: 0.7254 (m-70) cc_final: 0.6687 (m170) REVERT: B 32 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7587 (mt0) REVERT: B 54 MET cc_start: 0.7738 (tpp) cc_final: 0.7109 (tpp) REVERT: B 59 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 80 LYS cc_start: 0.8438 (mttt) cc_final: 0.7836 (mttt) REVERT: B 88 TYR cc_start: 0.7415 (p90) cc_final: 0.7114 (p90) REVERT: B 111 MET cc_start: 0.6986 (ptm) cc_final: 0.6540 (ptm) REVERT: B 134 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6740 (mm-30) REVERT: B 149 ARG cc_start: 0.7311 (ttt90) cc_final: 0.6749 (ttt-90) REVERT: B 168 VAL cc_start: 0.8158 (t) cc_final: 0.7863 (p) REVERT: B 171 ASP cc_start: 0.7328 (t0) cc_final: 0.6712 (t0) REVERT: B 172 PHE cc_start: 0.8027 (m-10) cc_final: 0.7418 (m-10) REVERT: B 210 LEU cc_start: 0.8344 (mm) cc_final: 0.7729 (tp) REVERT: B 252 ARG cc_start: 0.7236 (ttt-90) cc_final: 0.6826 (ttp80) REVERT: B 260 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.4794 (m) REVERT: B 278 ASP cc_start: 0.7215 (m-30) cc_final: 0.6654 (m-30) REVERT: B 286 SER cc_start: 0.6841 (m) cc_final: 0.6493 (m) REVERT: B 325 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7797 (mmtp) REVERT: B 357 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7916 (mtmm) REVERT: B 364 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8409 (m) REVERT: B 368 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: B 382 THR cc_start: 0.2813 (OUTLIER) cc_final: 0.2561 (m) REVERT: B 396 LYS cc_start: 0.7751 (mttt) cc_final: 0.7180 (mttm) REVERT: B 399 LYS cc_start: 0.6895 (mtpp) cc_final: 0.6397 (mtpp) REVERT: B 404 PHE cc_start: 0.8036 (p90) cc_final: 0.7549 (p90) REVERT: B 454 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7514 (mmtt) REVERT: B 458 ASP cc_start: 0.7662 (t0) cc_final: 0.6816 (t0) REVERT: B 487 LYS cc_start: 0.7679 (pttp) cc_final: 0.7273 (pttp) REVERT: B 521 ARG cc_start: 0.7490 (ppt-90) cc_final: 0.6678 (tmm-80) REVERT: B 534 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 553 SER cc_start: 0.8102 (m) cc_final: 0.7844 (t) REVERT: B 559 HIS cc_start: 0.7395 (t-90) cc_final: 0.6950 (t-90) REVERT: B 618 HIS cc_start: 0.7378 (m-70) cc_final: 0.6888 (m-70) outliers start: 32 outliers final: 17 residues processed: 317 average time/residue: 0.2741 time to fit residues: 113.7025 Evaluate side-chains 319 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 295 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.0270 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 361 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10276 Z= 0.212 Angle : 0.694 12.141 13896 Z= 0.338 Chirality : 0.049 0.334 1550 Planarity : 0.004 0.037 1814 Dihedral : 7.792 55.833 1620 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 2.59 % Allowed : 16.70 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.88 (0.23), residues: 1272 helix: -1.02 (0.88), residues: 40 sheet: -1.92 (0.64), residues: 58 loop : -1.36 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 49 HIS 0.005 0.001 HIS A 433 PHE 0.024 0.002 PHE A 172 TYR 0.021 0.001 TYR C 37 ARG 0.007 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 303 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7307 (mttp) cc_final: 0.7072 (mttp) REVERT: A 46 ASP cc_start: 0.7332 (m-30) cc_final: 0.6890 (m-30) REVERT: A 54 MET cc_start: 0.7631 (tpp) cc_final: 0.7135 (tpp) REVERT: A 58 CYS cc_start: 0.5294 (t) cc_final: 0.4927 (t) REVERT: A 59 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 64 ASN cc_start: 0.8189 (m-40) cc_final: 0.7503 (m110) REVERT: A 80 LYS cc_start: 0.8195 (mttt) cc_final: 0.7759 (mtmt) REVERT: A 83 GLN cc_start: 0.7490 (mt0) cc_final: 0.6600 (mt0) REVERT: A 111 MET cc_start: 0.7365 (ptm) cc_final: 0.7137 (ptm) REVERT: A 124 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: A 125 TYR cc_start: 0.7817 (p90) cc_final: 0.7604 (p90) REVERT: A 137 MET cc_start: 0.7373 (mtp) cc_final: 0.7143 (mtm) REVERT: A 149 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6777 (ttt-90) REVERT: A 168 VAL cc_start: 0.8456 (t) cc_final: 0.8106 (p) REVERT: A 252 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.6761 (mtp-110) REVERT: A 256 ASP cc_start: 0.6958 (m-30) cc_final: 0.6649 (m-30) REVERT: A 299 TYR cc_start: 0.7972 (m-80) cc_final: 0.7290 (m-80) REVERT: A 335 LYS cc_start: 0.7465 (tptp) cc_final: 0.7191 (tptp) REVERT: A 350 SER cc_start: 0.7121 (t) cc_final: 0.6852 (p) REVERT: A 357 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7702 (mtmm) REVERT: A 399 LYS cc_start: 0.7044 (mtpp) cc_final: 0.6578 (mtpp) REVERT: A 408 GLN cc_start: 0.7856 (mt0) cc_final: 0.7103 (tt0) REVERT: A 451 ARG cc_start: 0.7233 (ptp90) cc_final: 0.6961 (ptp90) REVERT: A 454 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7426 (mmtt) REVERT: A 458 ASP cc_start: 0.7644 (t0) cc_final: 0.7071 (t0) REVERT: A 460 ASP cc_start: 0.6535 (m-30) cc_final: 0.6204 (m-30) REVERT: A 489 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7628 (mtmt) REVERT: A 522 ASP cc_start: 0.6733 (t0) cc_final: 0.5637 (t0) REVERT: A 548 GLU cc_start: 0.4235 (mp0) cc_final: 0.3975 (mp0) REVERT: A 586 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6952 (tp) REVERT: A 618 HIS cc_start: 0.7239 (m-70) cc_final: 0.6677 (m170) REVERT: D 37 TYR cc_start: 0.8227 (m-10) cc_final: 0.8013 (m-10) REVERT: B 32 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: B 54 MET cc_start: 0.7672 (tpp) cc_final: 0.7181 (tpp) REVERT: B 59 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7111 (mt-10) REVERT: B 66 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: B 80 LYS cc_start: 0.8423 (mttt) cc_final: 0.7840 (mttt) REVERT: B 88 TYR cc_start: 0.7449 (p90) cc_final: 0.7120 (p90) REVERT: B 111 MET cc_start: 0.6954 (ptm) cc_final: 0.6514 (ptm) REVERT: B 134 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6771 (mm-30) REVERT: B 139 ASN cc_start: 0.7836 (m110) cc_final: 0.7574 (m-40) REVERT: B 149 ARG cc_start: 0.7293 (ttt90) cc_final: 0.6651 (ttt-90) REVERT: B 168 VAL cc_start: 0.8176 (t) cc_final: 0.7854 (p) REVERT: B 171 ASP cc_start: 0.7349 (t0) cc_final: 0.6729 (t0) REVERT: B 172 PHE cc_start: 0.8002 (m-10) cc_final: 0.7418 (m-10) REVERT: B 210 LEU cc_start: 0.8345 (mm) cc_final: 0.7722 (tp) REVERT: B 252 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6853 (ttp80) REVERT: B 253 LYS cc_start: 0.8111 (tttp) cc_final: 0.7840 (tttm) REVERT: B 261 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6920 (mmtt) REVERT: B 263 THR cc_start: 0.8456 (m) cc_final: 0.8198 (p) REVERT: B 278 ASP cc_start: 0.7239 (m-30) cc_final: 0.6703 (m-30) REVERT: B 286 SER cc_start: 0.6831 (m) cc_final: 0.6496 (m) REVERT: B 325 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7876 (mmtp) REVERT: B 350 SER cc_start: 0.7115 (t) cc_final: 0.6851 (p) REVERT: B 357 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7962 (mtmm) REVERT: B 361 ASN cc_start: 0.7210 (m-40) cc_final: 0.6793 (t0) REVERT: B 364 SER cc_start: 0.8807 (p) cc_final: 0.8391 (m) REVERT: B 368 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: B 382 THR cc_start: 0.3004 (OUTLIER) cc_final: 0.2763 (m) REVERT: B 396 LYS cc_start: 0.7758 (mttt) cc_final: 0.7162 (mttm) REVERT: B 399 LYS cc_start: 0.6950 (mtpp) cc_final: 0.6453 (mtpp) REVERT: B 404 PHE cc_start: 0.8041 (p90) cc_final: 0.7665 (p90) REVERT: B 454 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7504 (mmtt) REVERT: B 458 ASP cc_start: 0.7591 (t0) cc_final: 0.7054 (t0) REVERT: B 487 LYS cc_start: 0.7741 (pttp) cc_final: 0.7437 (pttp) REVERT: B 521 ARG cc_start: 0.7528 (ppt-90) cc_final: 0.7025 (ppt-90) REVERT: B 534 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: B 548 GLU cc_start: 0.5608 (mp0) cc_final: 0.5135 (mp0) REVERT: B 553 SER cc_start: 0.8136 (m) cc_final: 0.7874 (t) REVERT: B 557 GLN cc_start: 0.7448 (mt0) cc_final: 0.6971 (mm-40) REVERT: B 559 HIS cc_start: 0.7180 (t-90) cc_final: 0.6805 (t-90) REVERT: B 618 HIS cc_start: 0.7330 (m-70) cc_final: 0.6832 (m90) outliers start: 29 outliers final: 15 residues processed: 316 average time/residue: 0.2951 time to fit residues: 120.8771 Evaluate side-chains 317 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 121 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10276 Z= 0.271 Angle : 0.709 10.368 13896 Z= 0.347 Chirality : 0.050 0.331 1550 Planarity : 0.004 0.035 1814 Dihedral : 7.596 55.550 1620 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.65 % Favored : 91.12 % Rotamer: Outliers : 2.32 % Allowed : 17.05 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.81 (0.23), residues: 1272 helix: -1.25 (0.84), residues: 40 sheet: -1.70 (0.59), residues: 74 loop : -1.30 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 49 HIS 0.005 0.001 HIS B 559 PHE 0.027 0.002 PHE A 172 TYR 0.012 0.002 TYR C 37 ARG 0.006 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7347 (mttp) cc_final: 0.7114 (mttp) REVERT: A 32 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7292 (mt0) REVERT: A 58 CYS cc_start: 0.5488 (t) cc_final: 0.5060 (t) REVERT: A 59 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7019 (mt-10) REVERT: A 64 ASN cc_start: 0.8201 (m-40) cc_final: 0.7461 (m-40) REVERT: A 80 LYS cc_start: 0.8240 (mttt) cc_final: 0.7826 (mttt) REVERT: A 83 GLN cc_start: 0.7571 (mt0) cc_final: 0.6701 (mt0) REVERT: A 111 MET cc_start: 0.7327 (ptm) cc_final: 0.6957 (ptm) REVERT: A 124 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7761 (m-40) REVERT: A 137 MET cc_start: 0.7386 (mtp) cc_final: 0.7116 (mtm) REVERT: A 149 ARG cc_start: 0.7317 (ttt90) cc_final: 0.6862 (ttt90) REVERT: A 168 VAL cc_start: 0.8470 (t) cc_final: 0.8125 (p) REVERT: A 198 SER cc_start: 0.6321 (m) cc_final: 0.5951 (t) REVERT: A 210 LEU cc_start: 0.8396 (mm) cc_final: 0.8174 (mm) REVERT: A 256 ASP cc_start: 0.6999 (m-30) cc_final: 0.6715 (m-30) REVERT: A 299 TYR cc_start: 0.7986 (m-80) cc_final: 0.7600 (m-80) REVERT: A 309 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7346 (mtm-85) REVERT: A 335 LYS cc_start: 0.7472 (tptp) cc_final: 0.7200 (tptp) REVERT: A 350 SER cc_start: 0.7137 (t) cc_final: 0.6874 (p) REVERT: A 357 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7768 (mtmm) REVERT: A 361 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6867 (t0) REVERT: A 399 LYS cc_start: 0.7132 (mtpp) cc_final: 0.6650 (mtpp) REVERT: A 408 GLN cc_start: 0.7968 (mt0) cc_final: 0.7737 (mt0) REVERT: A 454 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7475 (mmtt) REVERT: A 458 ASP cc_start: 0.7676 (t0) cc_final: 0.7115 (t0) REVERT: A 489 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7676 (mtmt) REVERT: A 522 ASP cc_start: 0.6667 (t0) cc_final: 0.5731 (t0) REVERT: A 548 GLU cc_start: 0.4623 (mp0) cc_final: 0.4402 (mp0) REVERT: A 586 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 618 HIS cc_start: 0.7403 (m-70) cc_final: 0.6845 (m170) REVERT: D 37 TYR cc_start: 0.8288 (m-10) cc_final: 0.8075 (m-10) REVERT: B 32 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: B 54 MET cc_start: 0.7516 (tpp) cc_final: 0.7014 (tpp) REVERT: B 59 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7106 (mt-10) REVERT: B 66 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6401 (mt-10) REVERT: B 80 LYS cc_start: 0.8450 (mttt) cc_final: 0.7859 (mttt) REVERT: B 88 TYR cc_start: 0.7414 (p90) cc_final: 0.7169 (p90) REVERT: B 111 MET cc_start: 0.6955 (ptm) cc_final: 0.6534 (ptm) REVERT: B 134 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6775 (mm-30) REVERT: B 149 ARG cc_start: 0.7293 (ttt90) cc_final: 0.6694 (ttt-90) REVERT: B 168 VAL cc_start: 0.8175 (t) cc_final: 0.7840 (p) REVERT: B 171 ASP cc_start: 0.7403 (t0) cc_final: 0.6789 (t0) REVERT: B 172 PHE cc_start: 0.8055 (m-10) cc_final: 0.7454 (m-10) REVERT: B 210 LEU cc_start: 0.8354 (mm) cc_final: 0.7768 (tp) REVERT: B 252 ARG cc_start: 0.7166 (ttt-90) cc_final: 0.6814 (ttp80) REVERT: B 261 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7061 (mmtt) REVERT: B 263 THR cc_start: 0.8503 (m) cc_final: 0.8160 (p) REVERT: B 271 ASN cc_start: 0.7849 (t0) cc_final: 0.7500 (t0) REVERT: B 278 ASP cc_start: 0.7254 (m-30) cc_final: 0.6458 (m-30) REVERT: B 286 SER cc_start: 0.6776 (m) cc_final: 0.6442 (m) REVERT: B 293 LYS cc_start: 0.8368 (mttm) cc_final: 0.8131 (mttm) REVERT: B 325 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7865 (mmtp) REVERT: B 350 SER cc_start: 0.7123 (t) cc_final: 0.6868 (p) REVERT: B 361 ASN cc_start: 0.7235 (m-40) cc_final: 0.6772 (t0) REVERT: B 364 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8445 (m) REVERT: B 368 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: B 382 THR cc_start: 0.3334 (OUTLIER) cc_final: 0.3098 (m) REVERT: B 396 LYS cc_start: 0.7738 (mttt) cc_final: 0.7174 (mttm) REVERT: B 399 LYS cc_start: 0.6930 (mtpp) cc_final: 0.6412 (mtpp) REVERT: B 404 PHE cc_start: 0.8041 (p90) cc_final: 0.7712 (p90) REVERT: B 454 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7517 (mmtt) REVERT: B 458 ASP cc_start: 0.7717 (t0) cc_final: 0.7145 (t0) REVERT: B 487 LYS cc_start: 0.7747 (pttp) cc_final: 0.7313 (pttp) REVERT: B 521 ARG cc_start: 0.7596 (ppt-90) cc_final: 0.6951 (ppt-90) REVERT: B 534 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: B 548 GLU cc_start: 0.5649 (mp0) cc_final: 0.4546 (mp0) REVERT: B 553 SER cc_start: 0.8206 (m) cc_final: 0.7926 (t) REVERT: B 559 HIS cc_start: 0.7408 (t-90) cc_final: 0.7031 (t-90) REVERT: B 618 HIS cc_start: 0.7412 (m-70) cc_final: 0.6888 (m90) outliers start: 26 outliers final: 12 residues processed: 317 average time/residue: 0.3036 time to fit residues: 123.9116 Evaluate side-chains 320 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 299 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 77 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 466 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10276 Z= 0.221 Angle : 0.705 11.200 13896 Z= 0.344 Chirality : 0.049 0.341 1550 Planarity : 0.004 0.057 1814 Dihedral : 7.311 55.422 1620 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.90 % Rotamer: Outliers : 2.50 % Allowed : 17.86 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.74 (0.24), residues: 1272 helix: -1.32 (0.86), residues: 40 sheet: -1.76 (0.58), residues: 74 loop : -1.23 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 49 HIS 0.004 0.001 HIS B 233 PHE 0.029 0.002 PHE A 172 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 305 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7335 (mttp) cc_final: 0.7092 (mttp) REVERT: A 32 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7229 (mt0) REVERT: A 54 MET cc_start: 0.7722 (tpp) cc_final: 0.7057 (tpp) REVERT: A 58 CYS cc_start: 0.5493 (t) cc_final: 0.5109 (t) REVERT: A 59 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7041 (mt-10) REVERT: A 64 ASN cc_start: 0.8211 (m-40) cc_final: 0.7552 (m110) REVERT: A 80 LYS cc_start: 0.8292 (mttt) cc_final: 0.7732 (mttt) REVERT: A 83 GLN cc_start: 0.7559 (mt0) cc_final: 0.6476 (mt0) REVERT: A 105 GLN cc_start: 0.8099 (mt0) cc_final: 0.7895 (mt0) REVERT: A 111 MET cc_start: 0.7280 (ptm) cc_final: 0.6905 (ptm) REVERT: A 137 MET cc_start: 0.7299 (mtp) cc_final: 0.7079 (mtm) REVERT: A 149 ARG cc_start: 0.7359 (ttt90) cc_final: 0.6815 (ttt90) REVERT: A 168 VAL cc_start: 0.8458 (t) cc_final: 0.8117 (p) REVERT: A 198 SER cc_start: 0.6251 (m) cc_final: 0.5929 (t) REVERT: A 210 LEU cc_start: 0.8427 (mm) cc_final: 0.8206 (mm) REVERT: A 223 CYS cc_start: 0.4654 (p) cc_final: 0.4454 (p) REVERT: A 253 LYS cc_start: 0.8189 (mttp) cc_final: 0.7877 (mttp) REVERT: A 256 ASP cc_start: 0.7021 (m-30) cc_final: 0.6753 (m-30) REVERT: A 309 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7216 (mtm-85) REVERT: A 335 LYS cc_start: 0.7558 (tptp) cc_final: 0.7284 (tptp) REVERT: A 350 SER cc_start: 0.7151 (t) cc_final: 0.6916 (p) REVERT: A 357 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7828 (mtmm) REVERT: A 360 LYS cc_start: 0.8028 (tppp) cc_final: 0.7822 (tppp) REVERT: A 399 LYS cc_start: 0.7096 (mtpp) cc_final: 0.6609 (mtpp) REVERT: A 408 GLN cc_start: 0.7937 (mt0) cc_final: 0.7555 (mt0) REVERT: A 454 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7476 (mmtt) REVERT: A 458 ASP cc_start: 0.7655 (t0) cc_final: 0.7057 (t0) REVERT: A 460 ASP cc_start: 0.6536 (m-30) cc_final: 0.6183 (m-30) REVERT: A 489 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7669 (mtmt) REVERT: A 522 ASP cc_start: 0.6635 (t0) cc_final: 0.6098 (t0) REVERT: A 586 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6819 (tp) REVERT: A 618 HIS cc_start: 0.7288 (m-70) cc_final: 0.6752 (m170) REVERT: B 32 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: B 59 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7135 (mt-10) REVERT: B 80 LYS cc_start: 0.8439 (mttt) cc_final: 0.7840 (mttt) REVERT: B 88 TYR cc_start: 0.7424 (p90) cc_final: 0.7212 (p90) REVERT: B 111 MET cc_start: 0.6889 (ptm) cc_final: 0.6511 (ptm) REVERT: B 134 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6796 (mm-30) REVERT: B 149 ARG cc_start: 0.7312 (ttt90) cc_final: 0.6661 (ttt-90) REVERT: B 168 VAL cc_start: 0.8174 (t) cc_final: 0.7809 (p) REVERT: B 171 ASP cc_start: 0.7437 (t0) cc_final: 0.6821 (t0) REVERT: B 172 PHE cc_start: 0.7943 (m-10) cc_final: 0.7351 (m-10) REVERT: B 210 LEU cc_start: 0.8324 (mm) cc_final: 0.7763 (tp) REVERT: B 235 GLN cc_start: 0.6856 (mp10) cc_final: 0.6468 (mp10) REVERT: B 252 ARG cc_start: 0.7112 (ttt-90) cc_final: 0.6793 (ttp80) REVERT: B 261 LYS cc_start: 0.7410 (mmtt) cc_final: 0.6923 (mmtt) REVERT: B 263 THR cc_start: 0.8464 (m) cc_final: 0.8211 (p) REVERT: B 271 ASN cc_start: 0.7841 (t0) cc_final: 0.7498 (t0) REVERT: B 278 ASP cc_start: 0.7269 (m-30) cc_final: 0.6419 (m-30) REVERT: B 286 SER cc_start: 0.6731 (m) cc_final: 0.6406 (m) REVERT: B 293 LYS cc_start: 0.8346 (mttm) cc_final: 0.8116 (mttm) REVERT: B 325 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7881 (mmtp) REVERT: B 350 SER cc_start: 0.7134 (t) cc_final: 0.6909 (p) REVERT: B 361 ASN cc_start: 0.7195 (m-40) cc_final: 0.6763 (t0) REVERT: B 364 SER cc_start: 0.8799 (p) cc_final: 0.8420 (m) REVERT: B 368 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: B 396 LYS cc_start: 0.7740 (mttt) cc_final: 0.7157 (mttm) REVERT: B 399 LYS cc_start: 0.6981 (mtpp) cc_final: 0.6469 (mtpp) REVERT: B 404 PHE cc_start: 0.8084 (p90) cc_final: 0.7640 (p90) REVERT: B 432 GLN cc_start: 0.6601 (tp-100) cc_final: 0.6386 (tt0) REVERT: B 436 PHE cc_start: 0.7020 (m-80) cc_final: 0.6704 (m-80) REVERT: B 454 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7521 (mmtt) REVERT: B 458 ASP cc_start: 0.7654 (t0) cc_final: 0.7069 (t0) REVERT: B 487 LYS cc_start: 0.7756 (pttp) cc_final: 0.7323 (pttp) REVERT: B 521 ARG cc_start: 0.7604 (ppt-90) cc_final: 0.7245 (ptt-90) REVERT: B 534 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: B 553 SER cc_start: 0.8219 (m) cc_final: 0.7943 (t) REVERT: B 559 HIS cc_start: 0.7387 (t-90) cc_final: 0.7159 (t-90) REVERT: B 561 GLU cc_start: 0.6596 (tp30) cc_final: 0.6328 (tp30) REVERT: B 618 HIS cc_start: 0.7442 (m-70) cc_final: 0.6904 (m90) outliers start: 28 outliers final: 18 residues processed: 318 average time/residue: 0.2907 time to fit residues: 119.1773 Evaluate side-chains 317 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.0020 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10276 Z= 0.242 Angle : 0.720 11.872 13896 Z= 0.352 Chirality : 0.050 0.354 1550 Planarity : 0.004 0.056 1814 Dihedral : 7.097 55.189 1620 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.33 % Favored : 91.43 % Rotamer: Outliers : 2.50 % Allowed : 18.57 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.68 (0.24), residues: 1272 helix: -1.25 (0.89), residues: 38 sheet: -1.74 (0.58), residues: 74 loop : -1.18 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP C 49 HIS 0.006 0.001 HIS B 233 PHE 0.029 0.002 PHE A 172 TYR 0.023 0.002 TYR D 37 ARG 0.007 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 297 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7355 (mttp) cc_final: 0.7104 (mttp) REVERT: A 32 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7339 (mt0) REVERT: A 58 CYS cc_start: 0.5465 (t) cc_final: 0.5054 (t) REVERT: A 59 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 64 ASN cc_start: 0.8149 (m-40) cc_final: 0.7583 (m110) REVERT: A 80 LYS cc_start: 0.8277 (mttt) cc_final: 0.7721 (mttt) REVERT: A 83 GLN cc_start: 0.7596 (mt0) cc_final: 0.6680 (mt0) REVERT: A 111 MET cc_start: 0.7273 (ptm) cc_final: 0.6870 (ptm) REVERT: A 137 MET cc_start: 0.7315 (mtp) cc_final: 0.7094 (mtm) REVERT: A 149 ARG cc_start: 0.7364 (ttt90) cc_final: 0.6810 (ttt-90) REVERT: A 152 ASN cc_start: 0.7648 (t0) cc_final: 0.7436 (t0) REVERT: A 168 VAL cc_start: 0.8438 (t) cc_final: 0.8122 (p) REVERT: A 198 SER cc_start: 0.6353 (m) cc_final: 0.5985 (t) REVERT: A 210 LEU cc_start: 0.8484 (mm) cc_final: 0.8260 (mm) REVERT: A 223 CYS cc_start: 0.4732 (p) cc_final: 0.4517 (p) REVERT: A 252 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6845 (mtp-110) REVERT: A 256 ASP cc_start: 0.7041 (m-30) cc_final: 0.6764 (m-30) REVERT: A 299 TYR cc_start: 0.7999 (m-80) cc_final: 0.7699 (m-80) REVERT: A 335 LYS cc_start: 0.7474 (tptp) cc_final: 0.7222 (tptp) REVERT: A 350 SER cc_start: 0.7183 (t) cc_final: 0.6955 (p) REVERT: A 357 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7870 (mtmm) REVERT: A 399 LYS cc_start: 0.7163 (mtpp) cc_final: 0.6650 (mtpp) REVERT: A 454 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7416 (mmtt) REVERT: A 458 ASP cc_start: 0.7660 (t0) cc_final: 0.7077 (t0) REVERT: A 489 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7681 (mtmt) REVERT: A 586 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6740 (tp) REVERT: A 618 HIS cc_start: 0.7331 (m-70) cc_final: 0.6822 (m170) REVERT: D 37 TYR cc_start: 0.8172 (m-10) cc_final: 0.7904 (m-80) REVERT: D 51 GLU cc_start: 0.6264 (mp0) cc_final: 0.6058 (mp0) REVERT: B 29 LYS cc_start: 0.7029 (mttp) cc_final: 0.6778 (mttp) REVERT: B 32 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: B 54 MET cc_start: 0.7481 (tpp) cc_final: 0.6753 (tpp) REVERT: B 59 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7144 (mt-10) REVERT: B 80 LYS cc_start: 0.8482 (mttt) cc_final: 0.7900 (mttt) REVERT: B 88 TYR cc_start: 0.7444 (p90) cc_final: 0.7198 (p90) REVERT: B 111 MET cc_start: 0.6890 (ptm) cc_final: 0.6500 (ptm) REVERT: B 133 LYS cc_start: 0.7721 (tttp) cc_final: 0.7483 (tttp) REVERT: B 134 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: B 149 ARG cc_start: 0.7321 (ttt90) cc_final: 0.6754 (ttt-90) REVERT: B 168 VAL cc_start: 0.8169 (t) cc_final: 0.7796 (p) REVERT: B 171 ASP cc_start: 0.7501 (t0) cc_final: 0.6953 (t0) REVERT: B 172 PHE cc_start: 0.7956 (m-10) cc_final: 0.7360 (m-10) REVERT: B 210 LEU cc_start: 0.8315 (mm) cc_final: 0.7692 (tt) REVERT: B 235 GLN cc_start: 0.6684 (mp10) cc_final: 0.6398 (mp10) REVERT: B 252 ARG cc_start: 0.7029 (ttt-90) cc_final: 0.6701 (ttp80) REVERT: B 253 LYS cc_start: 0.8157 (tttp) cc_final: 0.7887 (tttp) REVERT: B 261 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6921 (mmtt) REVERT: B 263 THR cc_start: 0.8464 (m) cc_final: 0.8180 (p) REVERT: B 271 ASN cc_start: 0.7842 (t0) cc_final: 0.7466 (t0) REVERT: B 278 ASP cc_start: 0.7271 (m-30) cc_final: 0.6430 (m-30) REVERT: B 286 SER cc_start: 0.6722 (m) cc_final: 0.6421 (m) REVERT: B 293 LYS cc_start: 0.8355 (mttm) cc_final: 0.8111 (mttm) REVERT: B 325 LYS cc_start: 0.8069 (mmtp) cc_final: 0.7855 (mmtp) REVERT: B 350 SER cc_start: 0.7093 (t) cc_final: 0.6675 (p) REVERT: B 364 SER cc_start: 0.8777 (p) cc_final: 0.8383 (m) REVERT: B 368 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: B 396 LYS cc_start: 0.7727 (mttt) cc_final: 0.7263 (mttm) REVERT: B 399 LYS cc_start: 0.7023 (mtpp) cc_final: 0.6472 (mtpp) REVERT: B 404 PHE cc_start: 0.8050 (p90) cc_final: 0.7611 (p90) REVERT: B 432 GLN cc_start: 0.6613 (tp-100) cc_final: 0.6401 (tt0) REVERT: B 436 PHE cc_start: 0.6975 (m-80) cc_final: 0.6701 (m-80) REVERT: B 454 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7523 (mmtt) REVERT: B 458 ASP cc_start: 0.7702 (t0) cc_final: 0.7097 (t0) REVERT: B 487 LYS cc_start: 0.7786 (pttp) cc_final: 0.7325 (pttp) REVERT: B 521 ARG cc_start: 0.7593 (ppt-90) cc_final: 0.7243 (ptt-90) REVERT: B 534 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: B 553 SER cc_start: 0.8236 (m) cc_final: 0.7954 (t) REVERT: B 559 HIS cc_start: 0.7507 (t-90) cc_final: 0.7251 (t-90) REVERT: B 618 HIS cc_start: 0.7390 (m-70) cc_final: 0.6824 (m90) outliers start: 28 outliers final: 19 residues processed: 310 average time/residue: 0.2832 time to fit residues: 114.6135 Evaluate side-chains 320 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 296 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.0370 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 99 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10276 Z= 0.224 Angle : 0.706 12.328 13896 Z= 0.347 Chirality : 0.049 0.341 1550 Planarity : 0.004 0.057 1814 Dihedral : 6.960 54.927 1620 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.94 % Favored : 91.82 % Rotamer: Outliers : 2.32 % Allowed : 18.04 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.24), residues: 1272 helix: -1.27 (0.89), residues: 38 sheet: -1.71 (0.58), residues: 74 loop : -1.12 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 49 HIS 0.004 0.001 HIS A 370 PHE 0.030 0.002 PHE A 172 TYR 0.011 0.001 TYR A 471 ARG 0.007 0.000 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 310 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7349 (mttp) cc_final: 0.7092 (mttp) REVERT: A 58 CYS cc_start: 0.5489 (t) cc_final: 0.5034 (t) REVERT: A 59 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 64 ASN cc_start: 0.8130 (m-40) cc_final: 0.7711 (m110) REVERT: A 80 LYS cc_start: 0.8262 (mttt) cc_final: 0.7740 (mtmt) REVERT: A 83 GLN cc_start: 0.7537 (mt0) cc_final: 0.6668 (mt0) REVERT: A 149 ARG cc_start: 0.7385 (ttt90) cc_final: 0.6735 (ttt90) REVERT: A 168 VAL cc_start: 0.8434 (t) cc_final: 0.8103 (p) REVERT: A 198 SER cc_start: 0.6377 (m) cc_final: 0.6033 (t) REVERT: A 210 LEU cc_start: 0.8512 (mm) cc_final: 0.8278 (mm) REVERT: A 235 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6810 (mm-40) REVERT: A 256 ASP cc_start: 0.7022 (m-30) cc_final: 0.6780 (m-30) REVERT: A 309 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7158 (ttm110) REVERT: A 335 LYS cc_start: 0.7468 (tptp) cc_final: 0.7204 (tptp) REVERT: A 357 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7858 (mtmm) REVERT: A 399 LYS cc_start: 0.7115 (mtpp) cc_final: 0.6532 (mtpp) REVERT: A 408 GLN cc_start: 0.7905 (mt0) cc_final: 0.7567 (mt0) REVERT: A 432 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6783 (tp40) REVERT: A 451 ARG cc_start: 0.7433 (ptp-110) cc_final: 0.6751 (ptp-110) REVERT: A 454 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7420 (mmtt) REVERT: A 458 ASP cc_start: 0.7706 (t0) cc_final: 0.7036 (t0) REVERT: A 489 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7677 (mtmt) REVERT: A 586 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6632 (tp) REVERT: A 618 HIS cc_start: 0.7370 (m-70) cc_final: 0.6888 (m170) REVERT: B 29 LYS cc_start: 0.7032 (mttp) cc_final: 0.6544 (mttp) REVERT: B 32 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: B 54 MET cc_start: 0.7335 (tpp) cc_final: 0.6902 (tpp) REVERT: B 59 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 80 LYS cc_start: 0.8480 (mttt) cc_final: 0.7894 (mttt) REVERT: B 88 TYR cc_start: 0.7457 (p90) cc_final: 0.7224 (p90) REVERT: B 111 MET cc_start: 0.6856 (ptm) cc_final: 0.6468 (ptm) REVERT: B 133 LYS cc_start: 0.7722 (tttp) cc_final: 0.7493 (tttp) REVERT: B 134 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: B 149 ARG cc_start: 0.7352 (ttt90) cc_final: 0.6732 (ttt-90) REVERT: B 168 VAL cc_start: 0.8163 (t) cc_final: 0.7781 (p) REVERT: B 171 ASP cc_start: 0.7488 (t0) cc_final: 0.7127 (t0) REVERT: B 210 LEU cc_start: 0.8262 (mm) cc_final: 0.7638 (tt) REVERT: B 235 GLN cc_start: 0.6532 (mp10) cc_final: 0.6326 (mp10) REVERT: B 252 ARG cc_start: 0.6989 (ttt-90) cc_final: 0.6710 (ttp80) REVERT: B 263 THR cc_start: 0.8445 (m) cc_final: 0.8173 (p) REVERT: B 271 ASN cc_start: 0.7823 (t0) cc_final: 0.7462 (t0) REVERT: B 278 ASP cc_start: 0.7253 (m-30) cc_final: 0.6420 (m-30) REVERT: B 286 SER cc_start: 0.6697 (m) cc_final: 0.6367 (m) REVERT: B 293 LYS cc_start: 0.8350 (mttm) cc_final: 0.8104 (mttm) REVERT: B 325 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7826 (mmtp) REVERT: B 350 SER cc_start: 0.7087 (t) cc_final: 0.6713 (p) REVERT: B 361 ASN cc_start: 0.7235 (m-40) cc_final: 0.6800 (t0) REVERT: B 364 SER cc_start: 0.8770 (p) cc_final: 0.8387 (m) REVERT: B 368 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: B 396 LYS cc_start: 0.7691 (mttt) cc_final: 0.7234 (mttm) REVERT: B 399 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6468 (mtpp) REVERT: B 404 PHE cc_start: 0.8044 (p90) cc_final: 0.7768 (p90) REVERT: B 436 PHE cc_start: 0.6851 (m-80) cc_final: 0.6619 (m-80) REVERT: B 454 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7518 (mmtt) REVERT: B 458 ASP cc_start: 0.7675 (t0) cc_final: 0.7043 (t0) REVERT: B 487 LYS cc_start: 0.7792 (pttp) cc_final: 0.7356 (pttp) REVERT: B 521 ARG cc_start: 0.7583 (ppt-90) cc_final: 0.7179 (ptt-90) REVERT: B 522 ASP cc_start: 0.6656 (m-30) cc_final: 0.6109 (m-30) REVERT: B 534 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 548 GLU cc_start: 0.5442 (mp0) cc_final: 0.4951 (mp0) REVERT: B 553 SER cc_start: 0.8279 (m) cc_final: 0.7976 (t) REVERT: B 559 HIS cc_start: 0.7397 (t-90) cc_final: 0.7135 (t-90) REVERT: B 561 GLU cc_start: 0.6825 (tp30) cc_final: 0.6215 (tm-30) REVERT: B 618 HIS cc_start: 0.7407 (m-70) cc_final: 0.6826 (m90) outliers start: 26 outliers final: 18 residues processed: 319 average time/residue: 0.2870 time to fit residues: 118.5715 Evaluate side-chains 317 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133416 restraints weight = 15003.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137743 restraints weight = 7588.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140643 restraints weight = 4625.154| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10276 Z= 0.283 Angle : 0.740 11.894 13896 Z= 0.365 Chirality : 0.051 0.341 1550 Planarity : 0.004 0.047 1814 Dihedral : 7.095 54.445 1620 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.36 % Favored : 90.41 % Rotamer: Outliers : 2.14 % Allowed : 18.57 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.67 (0.24), residues: 1272 helix: -1.34 (0.86), residues: 38 sheet: -2.01 (0.60), residues: 64 loop : -1.17 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 49 HIS 0.004 0.001 HIS A 370 PHE 0.028 0.002 PHE A 172 TYR 0.012 0.002 TYR A 471 ARG 0.007 0.001 ARG A 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2894.27 seconds wall clock time: 52 minutes 37.00 seconds (3157.00 seconds total)