Starting phenix.real_space_refine on Thu Jun 12 12:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.map" model { file = "/net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvi_26141/06_2025/7tvi_26141.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 8965 2.51 5 N 2221 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13746 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2749 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "C" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2723 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2731 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2696 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 16, 'TRANS': 315} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: 9.21, per 1000 atoms: 0.67 Number of scatterers: 13746 At special positions: 0 Unit cell: (92.4, 93.5, 135.3, 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 89 16.00 O 2471 8.00 N 2221 7.00 C 8965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS E 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 62 " " NAG B 502 " - " ASN B 62 " " NAG C 501 " - " ASN C 62 " " NAG D 502 " - " ASN D 62 " " NAG E 601 " - " ASN E 54 " " NAG E 602 " - " ASN E 241 " Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 2.0 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 24 sheets defined 36.6% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.709A pdb=" N LEU A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.855A pdb=" N LEU A 114 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 116 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.621A pdb=" N VAL A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 4.615A pdb=" N ASN A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 297 removed outlier: 4.237A pdb=" N VAL A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 334 removed outlier: 3.685A pdb=" N ILE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 435 removed outlier: 3.563A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.604A pdb=" N TRP A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.730A pdb=" N LEU D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.598A pdb=" N ALA D 98 " --> pdb=" O PRO D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.567A pdb=" N MET D 113 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 117 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.525A pdb=" N LEU D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.551A pdb=" N ILE D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 removed outlier: 4.211A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 293 removed outlier: 3.805A pdb=" N LEU D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 332 removed outlier: 3.648A pdb=" N ILE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 436 removed outlier: 3.681A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.563A pdb=" N PHE D 422 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.912A pdb=" N ASP C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.685A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.752A pdb=" N TRP C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 272 through 296 removed outlier: 3.876A pdb=" N ARG C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 334 removed outlier: 3.757A pdb=" N TRP C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 433 removed outlier: 3.962A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.578A pdb=" N PHE C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 428 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 removed outlier: 3.512A pdb=" N ASP B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.603A pdb=" N ILE B 117 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.996A pdb=" N VAL B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.553A pdb=" N THR B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 334 removed outlier: 3.791A pdb=" N TRP B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 435 removed outlier: 4.085A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.941A pdb=" N PHE B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.534A pdb=" N MET E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.525A pdb=" N THR E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 removed outlier: 4.342A pdb=" N TRP E 288 " --> pdb=" O TRP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 316 removed outlier: 4.266A pdb=" N SER E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 354 removed outlier: 4.046A pdb=" N TRP E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 493 removed outlier: 4.916A pdb=" N ALA E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Proline residue: E 479 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.416A pdb=" N ASP A 81 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 75 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 83 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 71 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 87 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 69 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 67 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN A 91 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS A 65 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ASN A 93 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 63 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.502A pdb=" N GLU A 127 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA A 161 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 129 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 131 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 157 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A 81 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 75 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 83 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 71 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 87 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 69 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 67 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN A 91 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS A 65 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ASN A 93 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 63 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.571A pdb=" N ASP A 218 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.714A pdb=" N LYS A 224 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 106 through 108 removed outlier: 4.072A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.586A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 181 removed outlier: 3.595A pdb=" N GLU D 241 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 173 through 181 Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.791A pdb=" N ILE C 144 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.617A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'B' and resid 106 through 107 removed outlier: 4.452A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 83 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 74 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN B 85 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE B 72 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE B 87 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN B 70 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ARG B 89 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 68 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLN B 91 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN B 66 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN B 93 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N THR B 64 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.691A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 83 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 74 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN B 85 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE B 72 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE B 87 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN B 70 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ARG B 89 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 68 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLN B 91 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN B 66 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ASN B 93 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N THR B 64 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.661A pdb=" N GLU B 241 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 212 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 126 through 129 removed outlier: 4.265A pdb=" N LEU E 162 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE E 163 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP E 169 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP E 111 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER E 93 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN E 104 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE E 91 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE E 106 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN E 89 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ARG E 108 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE E 87 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG E 110 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN E 85 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ASN E 112 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ARG E 83 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL E 80 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET E 213 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP E 82 " --> pdb=" O MET E 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 147 through 152 removed outlier: 6.914A pdb=" N THR E 179 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA E 150 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER E 177 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE E 152 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ARG E 175 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP E 111 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER E 93 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN E 104 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE E 91 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE E 106 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN E 89 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ARG E 108 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N PHE E 87 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG E 110 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN E 85 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ASN E 112 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ARG E 83 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 142 through 144 removed outlier: 8.141A pdb=" N ILE E 258 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLU E 235 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR E 260 " --> pdb=" O LYS E 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 244 through 246 removed outlier: 3.679A pdb=" N TYR E 252 " --> pdb=" O LYS E 244 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1926 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: 5.07 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2307 1.32 - 1.45: 3822 1.45 - 1.57: 7813 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14089 Sorted by residual: bond pdb=" N GLY B 501 " pdb=" CA GLY B 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.94e+00 bond pdb=" N GLY D 503 " pdb=" CA GLY D 503 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.89e+00 bond pdb=" N GLY A 501 " pdb=" CA GLY A 501 " ideal model delta sigma weight residual 1.451 1.501 -0.050 1.60e-02 3.91e+03 9.68e+00 bond pdb=" N GLY D 501 " pdb=" CA GLY D 501 " ideal model delta sigma weight residual 1.451 1.500 -0.049 1.60e-02 3.91e+03 9.49e+00 bond pdb=" C PRO E 299 " pdb=" O PRO E 299 " ideal model delta sigma weight residual 1.237 1.202 0.036 1.20e-02 6.94e+03 8.87e+00 ... (remaining 14084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 18482 2.00 - 4.01: 511 4.01 - 6.01: 87 6.01 - 8.01: 33 8.01 - 10.01: 6 Bond angle restraints: 19119 Sorted by residual: angle pdb=" C PRO E 299 " pdb=" CA PRO E 299 " pdb=" CB PRO E 299 " ideal model delta sigma weight residual 112.55 103.39 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" N PRO D 274 " pdb=" CA PRO D 274 " pdb=" C PRO D 274 " ideal model delta sigma weight residual 113.53 107.59 5.94 1.39e+00 5.18e-01 1.83e+01 angle pdb=" C SER E 294 " pdb=" N ALA E 295 " pdb=" CA ALA E 295 " ideal model delta sigma weight residual 122.79 115.87 6.92 1.63e+00 3.76e-01 1.80e+01 angle pdb=" C ARG E 297 " pdb=" CA ARG E 297 " pdb=" CB ARG E 297 " ideal model delta sigma weight residual 110.79 117.58 -6.79 1.66e+00 3.63e-01 1.67e+01 angle pdb=" CA SER E 294 " pdb=" C SER E 294 " pdb=" O SER E 294 " ideal model delta sigma weight residual 120.82 116.54 4.28 1.05e+00 9.07e-01 1.66e+01 ... (remaining 19114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7639 17.98 - 35.95: 663 35.95 - 53.93: 114 53.93 - 71.91: 21 71.91 - 89.89: 12 Dihedral angle restraints: 8449 sinusoidal: 3474 harmonic: 4975 Sorted by residual: dihedral pdb=" CA MET B 287 " pdb=" C MET B 287 " pdb=" N THR B 288 " pdb=" CA THR B 288 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 182 " pdb=" SG CYS E 182 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual -86.00 -125.61 39.61 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA ALA E 327 " pdb=" C ALA E 327 " pdb=" N ILE E 328 " pdb=" CA ILE E 328 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1875 0.076 - 0.152: 264 0.152 - 0.227: 19 0.227 - 0.303: 4 0.303 - 0.379: 2 Chirality restraints: 2164 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ALA E 295 " pdb=" N ALA E 295 " pdb=" C ALA E 295 " pdb=" CB ALA E 295 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2161 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 110 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 111 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 169 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO C 170 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 263 " 0.017 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP D 263 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 263 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 263 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 263 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 263 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 263 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 263 " 0.003 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2061 2.76 - 3.30: 12995 3.30 - 3.83: 21732 3.83 - 4.37: 25292 4.37 - 4.90: 43325 Nonbonded interactions: 105405 Sorted by model distance: nonbonded pdb=" OG1 THR E 206 " pdb=" OD1 ASP E 208 " model vdw 2.228 3.040 nonbonded pdb=" O LEU B 285 " pdb=" OG1 THR B 288 " model vdw 2.242 3.040 nonbonded pdb=" O ALA E 327 " pdb=" OH TYR E 489 " model vdw 2.305 3.040 nonbonded pdb=" O PRO C 60 " pdb=" O6 NAG C 501 " model vdw 2.320 3.040 nonbonded pdb=" NE2 HIS B 133 " pdb=" OG1 THR B 157 " model vdw 2.329 3.120 ... (remaining 105400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 334 or resid 403 through 435 or resid 502)) selection = (chain 'B' and (resid 33 through 334 or resid 403 through 435 or resid 502)) selection = (chain 'C' and (resid 33 through 334 or resid 403 through 435 or resid 501)) selection = (chain 'D' and (resid 33 through 334 or resid 403 through 435 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.430 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14097 Z= 0.215 Angle : 0.840 16.127 19141 Z= 0.439 Chirality : 0.053 0.379 2164 Planarity : 0.006 0.076 2384 Dihedral : 14.018 89.886 5215 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1662 helix: 0.33 (0.23), residues: 458 sheet: 0.42 (0.27), residues: 380 loop : -1.56 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.029 0.002 PHE E 480 TYR 0.021 0.002 TYR A 82 ARG 0.006 0.001 ARG A 96 Details of bonding type rmsd link_NAG-ASN : bond 0.01275 ( 6) link_NAG-ASN : angle 5.71329 ( 18) hydrogen bonds : bond 0.29897 ( 554) hydrogen bonds : angle 7.57087 ( 1926) SS BOND : bond 0.00026 ( 2) SS BOND : angle 1.06914 ( 4) covalent geometry : bond 0.00463 (14089) covalent geometry : angle 0.82172 (19119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 PRO cc_start: 0.6032 (Cg_exo) cc_final: 0.5744 (Cg_endo) REVERT: A 179 GLN cc_start: 0.8283 (tt0) cc_final: 0.7915 (tp40) REVERT: A 181 GLU cc_start: 0.6269 (mp0) cc_final: 0.5937 (mp0) REVERT: A 235 GLU cc_start: 0.6392 (tt0) cc_final: 0.6185 (tt0) REVERT: A 419 PRO cc_start: 0.5881 (Cg_exo) cc_final: 0.5398 (Cg_endo) REVERT: D 114 LEU cc_start: 0.7925 (tt) cc_final: 0.7670 (tp) REVERT: D 210 GLN cc_start: 0.7981 (mp10) cc_final: 0.7327 (tt0) REVERT: D 300 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8421 (mmtm) REVERT: D 311 MET cc_start: 0.7492 (tpt) cc_final: 0.7256 (mmt) REVERT: D 403 PHE cc_start: 0.6854 (m-10) cc_final: 0.6156 (m-80) REVERT: C 123 PHE cc_start: 0.6475 (t80) cc_final: 0.6238 (t80) REVERT: C 270 MET cc_start: 0.7820 (mpp) cc_final: 0.7401 (mtm) REVERT: B 176 CYS cc_start: 0.7634 (m) cc_final: 0.7342 (m) REVERT: B 235 GLU cc_start: 0.6223 (tt0) cc_final: 0.5923 (tt0) REVERT: E 473 TYR cc_start: 0.6523 (p90) cc_final: 0.6123 (p90) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.2727 time to fit residues: 164.9948 Evaluate side-chains 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 125 optimal weight: 0.0000 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 250 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 131 ASN C 290 GLN B 243 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.143354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.119745 restraints weight = 27023.858| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.15 r_work: 0.3734 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14097 Z= 0.250 Angle : 0.860 12.098 19141 Z= 0.438 Chirality : 0.053 0.371 2164 Planarity : 0.006 0.059 2384 Dihedral : 6.398 58.681 1960 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.17 % Allowed : 12.83 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1662 helix: 0.51 (0.21), residues: 502 sheet: -0.20 (0.27), residues: 389 loop : -1.51 (0.19), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 118 HIS 0.007 0.001 HIS A 133 PHE 0.023 0.002 PHE A 238 TYR 0.040 0.002 TYR B 325 ARG 0.013 0.001 ARG B 276 Details of bonding type rmsd link_NAG-ASN : bond 0.01393 ( 6) link_NAG-ASN : angle 5.38709 ( 18) hydrogen bonds : bond 0.06420 ( 554) hydrogen bonds : angle 5.08792 ( 1926) SS BOND : bond 0.01162 ( 2) SS BOND : angle 1.50421 ( 4) covalent geometry : bond 0.00569 (14089) covalent geometry : angle 0.84441 (19119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 SER cc_start: 0.8435 (p) cc_final: 0.8138 (m) REVERT: D 210 GLN cc_start: 0.8418 (mp10) cc_final: 0.7713 (tt0) REVERT: D 251 MET cc_start: 0.7000 (mtp) cc_final: 0.6799 (mtt) REVERT: D 300 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8506 (mmtm) REVERT: D 403 PHE cc_start: 0.6777 (m-10) cc_final: 0.5930 (m-80) REVERT: B 37 PHE cc_start: 0.8877 (t80) cc_final: 0.8380 (t80) REVERT: B 113 MET cc_start: 0.7719 (ppp) cc_final: 0.6747 (ppp) REVERT: B 204 ASP cc_start: 0.7843 (p0) cc_final: 0.7351 (m-30) REVERT: E 132 LYS cc_start: 0.8439 (tptp) cc_final: 0.8215 (tptp) REVERT: E 185 ASP cc_start: 0.8254 (p0) cc_final: 0.7957 (p0) REVERT: E 256 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: E 345 GLU cc_start: 0.7487 (pp20) cc_final: 0.7134 (pp20) outliers start: 48 outliers final: 26 residues processed: 293 average time/residue: 0.2276 time to fit residues: 101.8496 Evaluate side-chains 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 148 optimal weight: 0.0870 chunk 35 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.143944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120538 restraints weight = 27139.351| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.24 r_work: 0.3746 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14097 Z= 0.135 Angle : 0.671 13.260 19141 Z= 0.333 Chirality : 0.046 0.286 2164 Planarity : 0.004 0.052 2384 Dihedral : 5.721 54.415 1958 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.25 % Allowed : 17.20 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1662 helix: 0.99 (0.22), residues: 501 sheet: 0.03 (0.27), residues: 386 loop : -1.42 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 118 HIS 0.003 0.001 HIS A 225 PHE 0.017 0.001 PHE C 319 TYR 0.019 0.001 TYR B 325 ARG 0.004 0.000 ARG A 276 Details of bonding type rmsd link_NAG-ASN : bond 0.01188 ( 6) link_NAG-ASN : angle 5.06183 ( 18) hydrogen bonds : bond 0.05334 ( 554) hydrogen bonds : angle 4.46182 ( 1926) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.21332 ( 4) covalent geometry : bond 0.00287 (14089) covalent geometry : angle 0.65307 (19119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7503 (mm110) cc_final: 0.7261 (mm-40) REVERT: D 210 GLN cc_start: 0.8470 (mp10) cc_final: 0.7931 (tt0) REVERT: D 289 THR cc_start: 0.8343 (m) cc_final: 0.8103 (p) REVERT: D 300 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8566 (mmtm) REVERT: D 403 PHE cc_start: 0.6497 (m-10) cc_final: 0.5658 (m-80) REVERT: B 37 PHE cc_start: 0.8911 (t80) cc_final: 0.8021 (t80) REVERT: B 113 MET cc_start: 0.7543 (ppp) cc_final: 0.6395 (ppp) REVERT: B 135 VAL cc_start: 0.7428 (OUTLIER) cc_final: 0.7121 (m) REVERT: B 204 ASP cc_start: 0.7794 (p0) cc_final: 0.7408 (m-30) REVERT: B 252 TYR cc_start: 0.7752 (m-80) cc_final: 0.7277 (m-80) REVERT: E 95 GLN cc_start: 0.8483 (pt0) cc_final: 0.7938 (pp30) REVERT: E 185 ASP cc_start: 0.8212 (p0) cc_final: 0.7921 (p0) REVERT: E 340 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.5776 (m-80) REVERT: E 352 MET cc_start: 0.8144 (ppp) cc_final: 0.6889 (mmt) outliers start: 34 outliers final: 22 residues processed: 270 average time/residue: 0.2887 time to fit residues: 121.0079 Evaluate side-chains 249 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 340 PHE Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN C 131 ASN C 139 ASN C 426 ASN B 179 GLN E 104 ASN E 153 HIS E 167 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107968 restraints weight = 27067.577| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.27 r_work: 0.3535 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 14097 Z= 0.282 Angle : 0.845 13.134 19141 Z= 0.435 Chirality : 0.052 0.369 2164 Planarity : 0.006 0.063 2384 Dihedral : 6.271 56.916 1958 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.50 % Allowed : 16.93 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1662 helix: 0.81 (0.22), residues: 504 sheet: -0.54 (0.27), residues: 381 loop : -1.57 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 310 HIS 0.011 0.002 HIS A 133 PHE 0.025 0.003 PHE D 123 TYR 0.028 0.003 TYR D 325 ARG 0.014 0.001 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00924 ( 6) link_NAG-ASN : angle 5.39568 ( 18) hydrogen bonds : bond 0.06219 ( 554) hydrogen bonds : angle 4.79941 ( 1926) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.77345 ( 4) covalent geometry : bond 0.00661 (14089) covalent geometry : angle 0.82909 (19119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7635 (mm110) cc_final: 0.7251 (mm-40) REVERT: D 81 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7695 (p0) REVERT: D 300 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8458 (mmtm) REVERT: D 311 MET cc_start: 0.8632 (mmt) cc_final: 0.8318 (mmt) REVERT: D 403 PHE cc_start: 0.6553 (m-10) cc_final: 0.5753 (m-80) REVERT: C 305 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7289 (mtpp) REVERT: C 335 HIS cc_start: 0.5814 (t70) cc_final: 0.5515 (m-70) REVERT: B 37 PHE cc_start: 0.9059 (t80) cc_final: 0.8590 (t80) REVERT: B 204 ASP cc_start: 0.7814 (p0) cc_final: 0.7516 (m-30) REVERT: B 250 GLN cc_start: 0.8658 (tp40) cc_final: 0.8418 (tp40) REVERT: B 269 ASN cc_start: 0.8055 (m-40) cc_final: 0.7459 (m-40) REVERT: B 433 TYR cc_start: 0.7604 (m-80) cc_final: 0.7363 (m-80) REVERT: E 185 ASP cc_start: 0.8254 (p0) cc_final: 0.8041 (p0) REVERT: E 252 TYR cc_start: 0.8619 (m-80) cc_final: 0.8056 (m-80) REVERT: E 340 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.5657 (m-80) outliers start: 68 outliers final: 47 residues processed: 280 average time/residue: 0.2207 time to fit residues: 95.5437 Evaluate side-chains 265 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 340 PHE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN E 104 ASN E 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.134186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111127 restraints weight = 26839.992| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.24 r_work: 0.3594 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14097 Z= 0.139 Angle : 0.674 13.298 19141 Z= 0.337 Chirality : 0.046 0.311 2164 Planarity : 0.004 0.046 2384 Dihedral : 5.739 56.018 1958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.10 % Allowed : 18.06 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1662 helix: 1.04 (0.22), residues: 499 sheet: -0.26 (0.27), residues: 380 loop : -1.46 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.017 0.001 PHE E 143 TYR 0.025 0.001 TYR D 325 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.01019 ( 6) link_NAG-ASN : angle 5.04755 ( 18) hydrogen bonds : bond 0.04746 ( 554) hydrogen bonds : angle 4.33613 ( 1926) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.45093 ( 4) covalent geometry : bond 0.00314 (14089) covalent geometry : angle 0.65667 (19119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7579 (mttp) REVERT: A 334 GLN cc_start: 0.7744 (mm110) cc_final: 0.7352 (mm-40) REVERT: D 81 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (p0) REVERT: D 263 TRP cc_start: 0.7602 (m100) cc_final: 0.7279 (m100) REVERT: D 300 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8408 (mmtm) REVERT: D 403 PHE cc_start: 0.6468 (m-10) cc_final: 0.5677 (m-80) REVERT: C 335 HIS cc_start: 0.5832 (t70) cc_final: 0.5464 (m-70) REVERT: B 37 PHE cc_start: 0.9076 (t80) cc_final: 0.8629 (t80) REVERT: B 135 VAL cc_start: 0.7672 (OUTLIER) cc_final: 0.7336 (m) REVERT: B 168 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8343 (p0) REVERT: B 204 ASP cc_start: 0.7881 (p0) cc_final: 0.7661 (m-30) REVERT: B 210 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6858 (tp-100) REVERT: B 250 GLN cc_start: 0.8621 (tp40) cc_final: 0.8395 (tp40) REVERT: B 269 ASN cc_start: 0.7944 (m-40) cc_final: 0.7514 (m-40) REVERT: B 433 TYR cc_start: 0.7577 (m-80) cc_final: 0.7286 (m-80) REVERT: E 270 MET cc_start: 0.8498 (tmm) cc_final: 0.7500 (mmt) REVERT: E 352 MET cc_start: 0.7903 (ppp) cc_final: 0.6992 (mmt) outliers start: 62 outliers final: 38 residues processed: 269 average time/residue: 0.2168 time to fit residues: 90.4985 Evaluate side-chains 252 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 0.0170 chunk 144 optimal weight: 1.9990 chunk 138 optimal weight: 0.0050 chunk 137 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN E 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.135659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112002 restraints weight = 27068.406| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.37 r_work: 0.3611 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14097 Z= 0.124 Angle : 0.649 13.341 19141 Z= 0.320 Chirality : 0.046 0.309 2164 Planarity : 0.004 0.043 2384 Dihedral : 5.425 54.768 1958 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.24 % Allowed : 19.31 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1662 helix: 1.09 (0.23), residues: 501 sheet: -0.02 (0.27), residues: 380 loop : -1.42 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 267 HIS 0.002 0.001 HIS A 225 PHE 0.015 0.001 PHE B 123 TYR 0.018 0.001 TYR D 325 ARG 0.005 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.01051 ( 6) link_NAG-ASN : angle 4.89238 ( 18) hydrogen bonds : bond 0.04278 ( 554) hydrogen bonds : angle 4.10259 ( 1926) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.34633 ( 4) covalent geometry : bond 0.00276 (14089) covalent geometry : angle 0.63143 (19119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8756 (t80) cc_final: 0.8554 (t80) REVERT: A 217 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7622 (mttp) REVERT: A 334 GLN cc_start: 0.7947 (mm110) cc_final: 0.7604 (mm-40) REVERT: D 81 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7631 (p0) REVERT: D 300 LYS cc_start: 0.8970 (mmtp) cc_final: 0.8430 (mmtm) REVERT: D 403 PHE cc_start: 0.6430 (m-10) cc_final: 0.5608 (m-80) REVERT: C 75 ILE cc_start: 0.9159 (mp) cc_final: 0.8893 (mt) REVERT: C 335 HIS cc_start: 0.6043 (t70) cc_final: 0.5617 (m-70) REVERT: B 37 PHE cc_start: 0.9124 (t80) cc_final: 0.8648 (t80) REVERT: B 135 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7312 (m) REVERT: B 168 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8209 (p0) REVERT: B 210 GLN cc_start: 0.7147 (tp-100) cc_final: 0.6920 (tp-100) REVERT: B 250 GLN cc_start: 0.8632 (tp40) cc_final: 0.8408 (tp40) REVERT: B 269 ASN cc_start: 0.7831 (m-40) cc_final: 0.7429 (m-40) REVERT: B 433 TYR cc_start: 0.7594 (m-80) cc_final: 0.7316 (m-80) REVERT: E 191 MET cc_start: 0.8487 (mpp) cc_final: 0.8239 (mpp) REVERT: E 223 ASP cc_start: 0.6361 (t70) cc_final: 0.5739 (t0) REVERT: E 270 MET cc_start: 0.8455 (tmm) cc_final: 0.7481 (mmt) REVERT: E 352 MET cc_start: 0.7988 (ppp) cc_final: 0.7218 (mmt) outliers start: 49 outliers final: 33 residues processed: 246 average time/residue: 0.2126 time to fit residues: 80.9869 Evaluate side-chains 242 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 152 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN E 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.135169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110920 restraints weight = 27073.837| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.22 r_work: 0.3603 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14097 Z= 0.128 Angle : 0.640 13.311 19141 Z= 0.315 Chirality : 0.045 0.314 2164 Planarity : 0.004 0.042 2384 Dihedral : 5.301 54.637 1958 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.31 % Allowed : 19.97 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1662 helix: 1.17 (0.23), residues: 501 sheet: 0.12 (0.28), residues: 378 loop : -1.39 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 310 HIS 0.003 0.001 HIS A 133 PHE 0.022 0.001 PHE E 189 TYR 0.021 0.001 TYR D 325 ARG 0.005 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.01022 ( 6) link_NAG-ASN : angle 4.82526 ( 18) hydrogen bonds : bond 0.04115 ( 554) hydrogen bonds : angle 4.00360 ( 1926) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.37248 ( 4) covalent geometry : bond 0.00292 (14089) covalent geometry : angle 0.62261 (19119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.8097 (mm110) cc_final: 0.7711 (mm110) REVERT: D 81 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7656 (p0) REVERT: D 300 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8425 (mmtm) REVERT: D 403 PHE cc_start: 0.6325 (m-10) cc_final: 0.5530 (m-80) REVERT: C 335 HIS cc_start: 0.6118 (t70) cc_final: 0.5745 (m-70) REVERT: B 37 PHE cc_start: 0.9159 (t80) cc_final: 0.8710 (t80) REVERT: B 113 MET cc_start: 0.7894 (ppp) cc_final: 0.7247 (ppp) REVERT: B 135 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7311 (m) REVERT: B 168 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8225 (p0) REVERT: B 269 ASN cc_start: 0.7716 (m-40) cc_final: 0.7364 (m-40) REVERT: E 223 ASP cc_start: 0.6348 (t70) cc_final: 0.5743 (t0) REVERT: E 270 MET cc_start: 0.8417 (tmm) cc_final: 0.7483 (mmt) outliers start: 50 outliers final: 36 residues processed: 248 average time/residue: 0.2275 time to fit residues: 86.2990 Evaluate side-chains 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 138 optimal weight: 0.0030 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 0.0770 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN E 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112518 restraints weight = 26874.722| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.21 r_work: 0.3623 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14097 Z= 0.118 Angle : 0.643 13.317 19141 Z= 0.316 Chirality : 0.045 0.310 2164 Planarity : 0.004 0.041 2384 Dihedral : 5.187 54.305 1958 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.17 % Allowed : 20.37 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1662 helix: 1.21 (0.23), residues: 504 sheet: 0.25 (0.28), residues: 376 loop : -1.40 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 310 HIS 0.002 0.001 HIS D 133 PHE 0.020 0.001 PHE E 189 TYR 0.022 0.001 TYR D 325 ARG 0.005 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.01057 ( 6) link_NAG-ASN : angle 4.76161 ( 18) hydrogen bonds : bond 0.03884 ( 554) hydrogen bonds : angle 3.88502 ( 1926) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.33794 ( 4) covalent geometry : bond 0.00258 (14089) covalent geometry : angle 0.62629 (19119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.8105 (mm110) cc_final: 0.7726 (mm110) REVERT: D 42 MET cc_start: 0.8161 (pmm) cc_final: 0.7347 (ptp) REVERT: D 81 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7661 (p0) REVERT: D 210 GLN cc_start: 0.8553 (mp10) cc_final: 0.8036 (tt0) REVERT: D 300 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8423 (mmtm) REVERT: D 403 PHE cc_start: 0.6304 (m-10) cc_final: 0.5509 (m-80) REVERT: C 335 HIS cc_start: 0.6185 (t70) cc_final: 0.5841 (m-70) REVERT: B 113 MET cc_start: 0.7850 (ppp) cc_final: 0.7298 (ppp) REVERT: B 135 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7291 (m) REVERT: B 168 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8227 (p0) REVERT: B 269 ASN cc_start: 0.7614 (m-40) cc_final: 0.7282 (m-40) REVERT: B 330 PHE cc_start: 0.7003 (t80) cc_final: 0.6741 (t80) REVERT: E 191 MET cc_start: 0.8389 (mpp) cc_final: 0.8178 (mpp) REVERT: E 223 ASP cc_start: 0.6276 (t70) cc_final: 0.5670 (t0) REVERT: E 270 MET cc_start: 0.8426 (tmm) cc_final: 0.7518 (mmt) REVERT: E 352 MET cc_start: 0.7879 (ppp) cc_final: 0.6933 (mmt) outliers start: 48 outliers final: 34 residues processed: 240 average time/residue: 0.2214 time to fit residues: 82.2163 Evaluate side-chains 235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 25 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN E 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.134878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110660 restraints weight = 26959.264| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.21 r_work: 0.3602 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14097 Z= 0.137 Angle : 0.657 13.188 19141 Z= 0.323 Chirality : 0.045 0.315 2164 Planarity : 0.004 0.042 2384 Dihedral : 5.200 54.668 1958 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 20.70 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1662 helix: 1.32 (0.23), residues: 497 sheet: 0.23 (0.28), residues: 377 loop : -1.42 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 310 HIS 0.005 0.001 HIS A 133 PHE 0.019 0.001 PHE E 189 TYR 0.023 0.001 TYR D 325 ARG 0.003 0.000 ARG B 415 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 6) link_NAG-ASN : angle 4.74167 ( 18) hydrogen bonds : bond 0.03953 ( 554) hydrogen bonds : angle 3.90944 ( 1926) SS BOND : bond 0.00251 ( 2) SS BOND : angle 0.49468 ( 4) covalent geometry : bond 0.00318 (14089) covalent geometry : angle 0.64065 (19119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.8134 (mm110) cc_final: 0.7857 (mm110) REVERT: D 42 MET cc_start: 0.8153 (pmm) cc_final: 0.7306 (ptp) REVERT: D 81 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7643 (p0) REVERT: D 300 LYS cc_start: 0.8933 (mmtp) cc_final: 0.8387 (mmtm) REVERT: D 403 PHE cc_start: 0.6452 (m-10) cc_final: 0.5666 (m-80) REVERT: C 335 HIS cc_start: 0.6224 (t70) cc_final: 0.5927 (m-70) REVERT: B 102 TYR cc_start: 0.6462 (m-10) cc_final: 0.6250 (m-10) REVERT: B 113 MET cc_start: 0.7887 (ppp) cc_final: 0.7345 (ppp) REVERT: B 135 VAL cc_start: 0.7619 (OUTLIER) cc_final: 0.7368 (m) REVERT: B 269 ASN cc_start: 0.7491 (m-40) cc_final: 0.7195 (m-40) REVERT: B 413 VAL cc_start: 0.7714 (t) cc_final: 0.7500 (p) REVERT: E 153 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8722 (m90) REVERT: E 213 MET cc_start: 0.7895 (ptm) cc_final: 0.7671 (ptp) REVERT: E 223 ASP cc_start: 0.6313 (t70) cc_final: 0.5734 (t0) REVERT: E 270 MET cc_start: 0.8416 (tmm) cc_final: 0.7566 (mmt) REVERT: E 352 MET cc_start: 0.7847 (ppp) cc_final: 0.7073 (mmt) outliers start: 43 outliers final: 36 residues processed: 235 average time/residue: 0.3098 time to fit residues: 113.1303 Evaluate side-chains 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 43 optimal weight: 0.0270 chunk 67 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.136699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112597 restraints weight = 26810.184| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.22 r_work: 0.3625 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14097 Z= 0.115 Angle : 0.647 13.237 19141 Z= 0.315 Chirality : 0.045 0.309 2164 Planarity : 0.003 0.042 2384 Dihedral : 5.093 54.043 1958 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.25 % Allowed : 21.30 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1662 helix: 1.36 (0.23), residues: 495 sheet: 0.36 (0.28), residues: 379 loop : -1.35 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 288 HIS 0.002 0.001 HIS D 133 PHE 0.018 0.001 PHE E 189 TYR 0.021 0.001 TYR D 325 ARG 0.006 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.01064 ( 6) link_NAG-ASN : angle 4.69449 ( 18) hydrogen bonds : bond 0.03731 ( 554) hydrogen bonds : angle 3.82323 ( 1926) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.33518 ( 4) covalent geometry : bond 0.00256 (14089) covalent geometry : angle 0.63148 (19119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 MET cc_start: 0.8153 (pmm) cc_final: 0.7352 (ptp) REVERT: D 81 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (p0) REVERT: D 210 GLN cc_start: 0.8637 (mp10) cc_final: 0.8124 (tt0) REVERT: D 300 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8398 (mmtm) REVERT: D 403 PHE cc_start: 0.6480 (m-10) cc_final: 0.5685 (m-80) REVERT: C 335 HIS cc_start: 0.6374 (t70) cc_final: 0.5970 (m-70) REVERT: B 113 MET cc_start: 0.7815 (ppp) cc_final: 0.7354 (ppp) REVERT: B 135 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7249 (m) REVERT: B 269 ASN cc_start: 0.7459 (m-40) cc_final: 0.7090 (p0) REVERT: B 330 PHE cc_start: 0.6894 (t80) cc_final: 0.6607 (t80) REVERT: B 413 VAL cc_start: 0.7820 (t) cc_final: 0.7604 (p) REVERT: E 153 HIS cc_start: 0.8957 (OUTLIER) cc_final: 0.8699 (m90) REVERT: E 223 ASP cc_start: 0.6201 (t70) cc_final: 0.5583 (t0) REVERT: E 270 MET cc_start: 0.8400 (tmm) cc_final: 0.7612 (mmt) REVERT: E 278 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8300 (mm) REVERT: E 352 MET cc_start: 0.7776 (ppp) cc_final: 0.7018 (mmt) outliers start: 34 outliers final: 27 residues processed: 229 average time/residue: 0.3377 time to fit residues: 122.7526 Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 426 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.132232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108555 restraints weight = 27144.637| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.29 r_work: 0.3557 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14097 Z= 0.178 Angle : 0.702 13.170 19141 Z= 0.350 Chirality : 0.047 0.330 2164 Planarity : 0.004 0.047 2384 Dihedral : 5.367 55.232 1958 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.98 % Allowed : 20.97 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1662 helix: 1.42 (0.23), residues: 496 sheet: 0.17 (0.28), residues: 376 loop : -1.46 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 310 HIS 0.004 0.001 HIS A 133 PHE 0.024 0.002 PHE E 189 TYR 0.023 0.002 TYR D 325 ARG 0.014 0.001 ARG C 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 6) link_NAG-ASN : angle 4.83431 ( 18) hydrogen bonds : bond 0.04278 ( 554) hydrogen bonds : angle 4.04873 ( 1926) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.71424 ( 4) covalent geometry : bond 0.00419 (14089) covalent geometry : angle 0.68660 (19119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7140.04 seconds wall clock time: 129 minutes 6.11 seconds (7746.11 seconds total)