Starting phenix.real_space_refine on Wed Mar 4 13:21:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tvi_26141/03_2026/7tvi_26141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvi_26141/03_2026/7tvi_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_26141/03_2026/7tvi_26141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvi_26141/03_2026/7tvi_26141.map" model { file = "/net/cci-nas-00/data/ceres_data/7tvi_26141/03_2026/7tvi_26141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvi_26141/03_2026/7tvi_26141.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.24 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: 0.79 Conformation dependent library (CDL) restraints added in 591.3 milliseconds 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: 0.39 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: 2.23 Time building geometry restraints manager: 1.08 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 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.790 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG A 96 TYR 0.021 0.002 TYR A 82 PHE 0.029 0.002 PHE E 480 TRP 0.039 0.002 TRP D 263 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00463 (14089) covalent geometry : angle 0.82172 (19119) SS BOND : bond 0.00026 ( 2) SS BOND : angle 1.06914 ( 4) hydrogen bonds : bond 0.29897 ( 554) hydrogen bonds : angle 7.57087 ( 1926) link_NAG-ASN : bond 0.01275 ( 6) link_NAG-ASN : angle 5.71329 ( 18) *********************** 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 : 0.509 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: 0.5938 (mp0) REVERT: A 235 GLU cc_start: 0.6392 (tt0) cc_final: 0.6185 (tt0) REVERT: A 268 ILE cc_start: 0.7606 (tp) cc_final: 0.7291 (tt) 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: 0.7255 (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: 0.6237 (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: 0.1109 time to fit residues: 67.7531 Evaluate side-chains 241 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 C 90 GLN C 131 ASN C 290 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.147474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124235 restraints weight = 27318.501| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.18 r_work: 0.3801 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14097 Z= 0.221 Angle : 0.814 12.467 19141 Z= 0.412 Chirality : 0.051 0.499 2164 Planarity : 0.005 0.059 2384 Dihedral : 6.210 57.412 1960 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.78 % Allowed : 12.63 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1662 helix: 0.82 (0.22), residues: 498 sheet: 0.14 (0.27), residues: 392 loop : -1.54 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 195 TYR 0.034 0.002 TYR B 325 PHE 0.022 0.002 PHE B 422 TRP 0.028 0.002 TRP A 118 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00495 (14089) covalent geometry : angle 0.79641 (19119) SS BOND : bond 0.01613 ( 2) SS BOND : angle 1.14829 ( 4) hydrogen bonds : bond 0.05985 ( 554) hydrogen bonds : angle 4.85133 ( 1926) link_NAG-ASN : bond 0.01221 ( 6) link_NAG-ASN : angle 5.55355 ( 18) *********************** 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 312 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 109 LEU cc_start: 0.7030 (mm) cc_final: 0.6532 (mp) REVERT: D 114 LEU cc_start: 0.8215 (tt) cc_final: 0.7851 (tp) REVERT: D 210 GLN cc_start: 0.8418 (mp10) cc_final: 0.7562 (tt0) REVERT: D 251 MET cc_start: 0.6995 (mtp) cc_final: 0.6786 (mtt) REVERT: D 300 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8702 (mppt) REVERT: D 403 PHE cc_start: 0.6696 (m-10) cc_final: 0.5866 (m-80) REVERT: B 37 PHE cc_start: 0.8850 (t80) cc_final: 0.8053 (t80) REVERT: B 113 MET cc_start: 0.7506 (ppp) cc_final: 0.6658 (ppp) REVERT: E 88 ILE cc_start: 0.8769 (pt) cc_final: 0.8368 (mm) REVERT: E 185 ASP cc_start: 0.8183 (p0) cc_final: 0.7878 (p0) REVERT: E 345 GLU cc_start: 0.7520 (pp20) cc_final: 0.7206 (pp20) outliers start: 42 outliers final: 23 residues processed: 295 average time/residue: 0.0983 time to fit residues: 44.7902 Evaluate side-chains 247 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU 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 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 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 211 GLN Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 312 CYS 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 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 134 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.144546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.121344 restraints weight = 27067.458| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.24 r_work: 0.3758 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14097 Z= 0.153 Angle : 0.679 13.275 19141 Z= 0.339 Chirality : 0.046 0.299 2164 Planarity : 0.004 0.049 2384 Dihedral : 5.600 53.767 1958 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.51 % Allowed : 16.34 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1662 helix: 1.15 (0.22), residues: 496 sheet: 0.16 (0.28), residues: 380 loop : -1.49 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.027 0.001 TYR B 325 PHE 0.021 0.001 PHE C 319 TRP 0.017 0.001 TRP A 118 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00343 (14089) covalent geometry : angle 0.66081 (19119) SS BOND : bond 0.00438 ( 2) SS BOND : angle 0.26908 ( 4) hydrogen bonds : bond 0.05520 ( 554) hydrogen bonds : angle 4.42235 ( 1926) link_NAG-ASN : bond 0.01112 ( 6) link_NAG-ASN : angle 5.11202 ( 18) *********************** 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 291 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7643 (mm110) cc_final: 0.7320 (mm-40) REVERT: D 210 GLN cc_start: 0.8413 (mp10) cc_final: 0.7741 (tt0) REVERT: D 300 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8580 (mmtm) REVERT: D 403 PHE cc_start: 0.6481 (m-10) cc_final: 0.5634 (m-80) REVERT: B 37 PHE cc_start: 0.8976 (t80) cc_final: 0.8252 (t80) REVERT: B 113 MET cc_start: 0.7600 (ppp) cc_final: 0.6546 (ppp) REVERT: B 135 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7164 (m) REVERT: B 204 ASP cc_start: 0.7869 (p0) cc_final: 0.7328 (m-30) REVERT: E 95 GLN cc_start: 0.8481 (pt0) cc_final: 0.7922 (pp30) REVERT: E 185 ASP cc_start: 0.8223 (p0) cc_final: 0.7919 (p0) REVERT: E 256 GLU cc_start: 0.6969 (mp0) cc_final: 0.6487 (mp0) REVERT: E 340 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: E 473 TYR cc_start: 0.6476 (p90) cc_final: 0.6077 (p90) outliers start: 38 outliers final: 24 residues processed: 274 average time/residue: 0.0941 time to fit residues: 40.4887 Evaluate side-chains 249 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 SER 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 D residue 322 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 403 PHE 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 239 TYR Chi-restraints excluded: chain E residue 251 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 5.9990 chunk 156 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN E 194 GLN E 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.138485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114642 restraints weight = 27165.653| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.20 r_work: 0.3653 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14097 Z= 0.172 Angle : 0.687 13.019 19141 Z= 0.345 Chirality : 0.047 0.300 2164 Planarity : 0.004 0.043 2384 Dihedral : 5.559 55.719 1958 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.76 % Allowed : 16.20 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1662 helix: 1.21 (0.22), residues: 499 sheet: -0.08 (0.27), residues: 386 loop : -1.39 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.023 0.002 TYR A 246 PHE 0.017 0.002 PHE A 238 TRP 0.012 0.001 TRP A 310 HIS 0.007 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00385 (14089) covalent geometry : angle 0.67094 (19119) SS BOND : bond 0.04341 ( 2) SS BOND : angle 0.27051 ( 4) hydrogen bonds : bond 0.04763 ( 554) hydrogen bonds : angle 4.24234 ( 1926) link_NAG-ASN : bond 0.01032 ( 6) link_NAG-ASN : angle 4.90245 ( 18) *********************** 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 312 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 240 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7776 (mm110) cc_final: 0.7450 (mm-40) REVERT: D 250 GLN cc_start: 0.8337 (tp40) cc_final: 0.8129 (tm-30) REVERT: D 251 MET cc_start: 0.7136 (mtp) cc_final: 0.6669 (mtt) REVERT: D 300 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8510 (mmtm) REVERT: D 403 PHE cc_start: 0.6447 (m-10) cc_final: 0.5690 (m-80) REVERT: B 37 PHE cc_start: 0.9055 (t80) cc_final: 0.8137 (t80) REVERT: B 135 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7069 (m) REVERT: B 204 ASP cc_start: 0.7731 (p0) cc_final: 0.7401 (m-30) REVERT: B 270 MET cc_start: 0.7535 (mmm) cc_final: 0.7010 (ptp) REVERT: B 334 GLN cc_start: 0.7684 (pm20) cc_final: 0.6895 (pm20) REVERT: E 95 GLN cc_start: 0.8552 (pt0) cc_final: 0.8009 (pp30) REVERT: E 185 ASP cc_start: 0.8171 (p0) cc_final: 0.7899 (p0) REVERT: E 340 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5633 (m-80) outliers start: 72 outliers final: 43 residues processed: 285 average time/residue: 0.0983 time to fit residues: 43.3039 Evaluate side-chains 267 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain C residue 115 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 411 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 VAL 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 210 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 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 285 LEU 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 149 optimal weight: 0.0670 chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 101 optimal weight: 0.0770 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116956 restraints weight = 26867.914| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.21 r_work: 0.3684 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14097 Z= 0.118 Angle : 0.635 13.318 19141 Z= 0.313 Chirality : 0.045 0.293 2164 Planarity : 0.004 0.041 2384 Dihedral : 5.316 54.759 1958 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.11 % Allowed : 17.99 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1662 helix: 1.26 (0.23), residues: 494 sheet: 0.21 (0.27), residues: 375 loop : -1.36 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.023 0.001 TYR D 325 PHE 0.016 0.001 PHE E 189 TRP 0.026 0.001 TRP B 310 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00247 (14089) covalent geometry : angle 0.61748 (19119) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.37556 ( 4) hydrogen bonds : bond 0.04233 ( 554) hydrogen bonds : angle 4.06503 ( 1926) link_NAG-ASN : bond 0.01062 ( 6) link_NAG-ASN : angle 4.83878 ( 18) *********************** 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 279 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8815 (mp) cc_final: 0.8585 (tp) REVERT: A 334 GLN cc_start: 0.7801 (mm110) cc_final: 0.7523 (mm-40) REVERT: D 210 GLN cc_start: 0.8751 (mp10) cc_final: 0.8013 (tt0) REVERT: D 300 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8546 (mmtm) REVERT: D 403 PHE cc_start: 0.6436 (m-10) cc_final: 0.5679 (m-80) REVERT: C 171 MET cc_start: 0.8356 (pmm) cc_final: 0.8117 (pmm) REVERT: B 37 PHE cc_start: 0.8995 (t80) cc_final: 0.8634 (t80) REVERT: B 135 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.7023 (m) REVERT: B 168 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8006 (p0) REVERT: B 204 ASP cc_start: 0.7636 (p0) cc_final: 0.7371 (m-30) REVERT: B 269 ASN cc_start: 0.7866 (m-40) cc_final: 0.7400 (m-40) REVERT: B 415 ARG cc_start: 0.6662 (mtp180) cc_final: 0.6361 (mtp85) REVERT: E 185 ASP cc_start: 0.8142 (p0) cc_final: 0.7875 (p0) REVERT: E 340 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: E 352 MET cc_start: 0.8038 (ppp) cc_final: 0.6977 (mmt) outliers start: 47 outliers final: 33 residues processed: 261 average time/residue: 0.0903 time to fit residues: 37.1466 Evaluate side-chains 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 248 LEU 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 418 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 285 LEU 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 421 VAL 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 257 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 270 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 46 optimal weight: 0.0770 chunk 164 optimal weight: 4.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.140798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.117143 restraints weight = 26850.487| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.18 r_work: 0.3695 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14097 Z= 0.114 Angle : 0.638 13.249 19141 Z= 0.312 Chirality : 0.045 0.293 2164 Planarity : 0.004 0.039 2384 Dihedral : 5.155 54.370 1958 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.24 % Allowed : 19.11 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1662 helix: 1.26 (0.23), residues: 498 sheet: 0.46 (0.28), residues: 369 loop : -1.31 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.022 0.001 TYR B 325 PHE 0.023 0.001 PHE E 189 TRP 0.016 0.001 TRP D 267 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00247 (14089) covalent geometry : angle 0.62122 (19119) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.29857 ( 4) hydrogen bonds : bond 0.03982 ( 554) hydrogen bonds : angle 3.91442 ( 1926) link_NAG-ASN : bond 0.01052 ( 6) link_NAG-ASN : angle 4.74712 ( 18) *********************** 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 286 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8827 (mp) cc_final: 0.8580 (tp) REVERT: A 334 GLN cc_start: 0.7912 (mm110) cc_final: 0.7600 (mm-40) REVERT: D 144 ILE cc_start: 0.8481 (pt) cc_final: 0.8222 (mt) REVERT: D 210 GLN cc_start: 0.8771 (mp10) cc_final: 0.8087 (tt0) REVERT: D 300 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8540 (mmtm) REVERT: D 403 PHE cc_start: 0.6620 (m-10) cc_final: 0.5815 (m-80) REVERT: C 171 MET cc_start: 0.8348 (pmm) cc_final: 0.8145 (pmm) REVERT: B 135 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7125 (m) REVERT: B 168 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7979 (p0) REVERT: B 204 ASP cc_start: 0.7731 (p0) cc_final: 0.7490 (m-30) REVERT: B 269 ASN cc_start: 0.7926 (m-40) cc_final: 0.7534 (m-40) REVERT: B 270 MET cc_start: 0.7527 (mmm) cc_final: 0.7103 (ptp) REVERT: B 413 VAL cc_start: 0.7191 (t) cc_final: 0.6987 (p) REVERT: B 415 ARG cc_start: 0.6693 (mtp180) cc_final: 0.6473 (mtp85) REVERT: E 185 ASP cc_start: 0.8212 (p0) cc_final: 0.7949 (p0) REVERT: E 340 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.5465 (m-80) REVERT: E 352 MET cc_start: 0.8018 (ppp) cc_final: 0.6951 (mmt) outliers start: 49 outliers final: 34 residues processed: 266 average time/residue: 0.0969 time to fit residues: 40.1894 Evaluate side-chains 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 THR 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 279 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 301 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 D residue 323 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 420 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 310 TRP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 229 GLN 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 270 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 138 optimal weight: 0.0070 chunk 161 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115753 restraints weight = 26976.808| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.20 r_work: 0.3675 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14097 Z= 0.121 Angle : 0.631 13.217 19141 Z= 0.308 Chirality : 0.045 0.298 2164 Planarity : 0.004 0.043 2384 Dihedral : 5.098 54.323 1958 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.78 % Allowed : 20.11 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1662 helix: 1.29 (0.23), residues: 497 sheet: 0.48 (0.28), residues: 364 loop : -1.29 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.021 0.001 TYR E 473 PHE 0.018 0.001 PHE E 189 TRP 0.011 0.001 TRP A 310 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00272 (14089) covalent geometry : angle 0.61425 (19119) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.44434 ( 4) hydrogen bonds : bond 0.03852 ( 554) hydrogen bonds : angle 3.88754 ( 1926) link_NAG-ASN : bond 0.01034 ( 6) link_NAG-ASN : angle 4.70295 ( 18) *********************** 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 270 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8815 (mp) cc_final: 0.8588 (tp) REVERT: A 334 GLN cc_start: 0.7918 (mm110) cc_final: 0.7487 (mm-40) REVERT: D 144 ILE cc_start: 0.8556 (pt) cc_final: 0.8348 (mt) REVERT: D 300 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8465 (mmtm) REVERT: D 403 PHE cc_start: 0.6625 (m-10) cc_final: 0.5816 (m-80) REVERT: C 171 MET cc_start: 0.8376 (pmm) cc_final: 0.8139 (pmm) REVERT: B 113 MET cc_start: 0.7840 (ppp) cc_final: 0.6958 (ppp) REVERT: B 135 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7217 (m) REVERT: B 168 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8096 (p0) REVERT: B 269 ASN cc_start: 0.7866 (m-40) cc_final: 0.7572 (m-40) REVERT: B 300 LYS cc_start: 0.8418 (tttt) cc_final: 0.8163 (tttp) REVERT: B 413 VAL cc_start: 0.7341 (t) cc_final: 0.7128 (p) REVERT: E 185 ASP cc_start: 0.8283 (p0) cc_final: 0.8023 (p0) REVERT: E 352 MET cc_start: 0.7895 (ppp) cc_final: 0.7494 (ppp) outliers start: 42 outliers final: 30 residues processed: 256 average time/residue: 0.0923 time to fit residues: 37.0011 Evaluate side-chains 251 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 THR 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 279 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 285 LEU Chi-restraints excluded: chain C residue 420 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 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 193 THR Chi-restraints excluded: chain E residue 210 LEU 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 270 MET Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.0010 chunk 149 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.140243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116513 restraints weight = 26886.787| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.21 r_work: 0.3681 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14097 Z= 0.112 Angle : 0.633 13.192 19141 Z= 0.306 Chirality : 0.045 0.428 2164 Planarity : 0.004 0.055 2384 Dihedral : 5.017 54.214 1958 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.78 % Allowed : 20.90 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1662 helix: 1.28 (0.23), residues: 499 sheet: 0.43 (0.28), residues: 369 loop : -1.24 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.018 0.001 TYR E 473 PHE 0.019 0.001 PHE E 189 TRP 0.013 0.001 TRP D 267 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00244 (14089) covalent geometry : angle 0.61717 (19119) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.30045 ( 4) hydrogen bonds : bond 0.03701 ( 554) hydrogen bonds : angle 3.83382 ( 1926) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 4.66676 ( 18) *********************** 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 276 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8831 (mp) cc_final: 0.8572 (tp) REVERT: A 334 GLN cc_start: 0.7943 (mm110) cc_final: 0.7526 (mm-40) REVERT: D 210 GLN cc_start: 0.8662 (mp10) cc_final: 0.8088 (tt0) REVERT: D 300 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8471 (mmtm) REVERT: D 403 PHE cc_start: 0.6628 (m-10) cc_final: 0.5822 (m-80) REVERT: C 171 MET cc_start: 0.8386 (pmm) cc_final: 0.8117 (pmm) REVERT: B 37 PHE cc_start: 0.9054 (t80) cc_final: 0.8478 (t80) REVERT: B 113 MET cc_start: 0.7899 (ppp) cc_final: 0.7238 (ppp) REVERT: B 135 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7164 (m) REVERT: B 168 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8101 (p0) REVERT: B 269 ASN cc_start: 0.7771 (m-40) cc_final: 0.7403 (m-40) REVERT: B 413 VAL cc_start: 0.7370 (t) cc_final: 0.7138 (p) REVERT: E 185 ASP cc_start: 0.8257 (p0) cc_final: 0.7994 (p0) REVERT: E 223 ASP cc_start: 0.6363 (t0) cc_final: 0.5877 (t0) outliers start: 42 outliers final: 32 residues processed: 261 average time/residue: 0.0958 time to fit residues: 39.2441 Evaluate side-chains 255 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 279 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 110 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 420 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 257 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 210 LEU 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 270 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 60 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.138181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.114033 restraints weight = 26895.814| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.22 r_work: 0.3650 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7046 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= 0.126 Angle : 0.650 13.110 19141 Z= 0.317 Chirality : 0.045 0.404 2164 Planarity : 0.004 0.055 2384 Dihedral : 5.053 54.406 1958 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.71 % Allowed : 20.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1662 helix: 1.21 (0.23), residues: 507 sheet: 0.47 (0.28), residues: 365 loop : -1.22 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 102 TYR 0.024 0.001 TYR B 102 PHE 0.020 0.001 PHE E 189 TRP 0.014 0.001 TRP A 310 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00291 (14089) covalent geometry : angle 0.63407 (19119) SS BOND : bond 0.00405 ( 2) SS BOND : angle 0.47522 ( 4) hydrogen bonds : bond 0.03790 ( 554) hydrogen bonds : angle 3.85913 ( 1926) link_NAG-ASN : bond 0.01033 ( 6) link_NAG-ASN : angle 4.66047 ( 18) *********************** 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 257 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.6386 (mmm) cc_final: 0.6042 (mmt) REVERT: A 257 LEU cc_start: 0.8860 (mp) cc_final: 0.8649 (tp) REVERT: A 334 GLN cc_start: 0.8032 (mm110) cc_final: 0.7613 (mm110) REVERT: D 210 GLN cc_start: 0.8678 (mp10) cc_final: 0.8050 (tt0) REVERT: D 300 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8432 (mmtm) REVERT: D 403 PHE cc_start: 0.6621 (m-10) cc_final: 0.5813 (m-80) REVERT: C 171 MET cc_start: 0.8369 (pmm) cc_final: 0.8165 (pmm) REVERT: B 37 PHE cc_start: 0.9149 (t80) cc_final: 0.8772 (t80) REVERT: B 135 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7273 (m) REVERT: B 168 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 269 ASN cc_start: 0.7680 (m-40) cc_final: 0.7206 (t0) REVERT: B 270 MET cc_start: 0.7442 (mmm) cc_final: 0.6965 (ptp) REVERT: B 271 ASP cc_start: 0.8563 (p0) cc_final: 0.8355 (p0) REVERT: B 300 LYS cc_start: 0.8199 (tttt) cc_final: 0.7813 (tttp) REVERT: B 413 VAL cc_start: 0.7533 (t) cc_final: 0.7289 (p) REVERT: E 185 ASP cc_start: 0.8301 (p0) cc_final: 0.8056 (p0) REVERT: E 223 ASP cc_start: 0.6275 (t0) cc_final: 0.5822 (t0) REVERT: E 270 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7362 (mmt) outliers start: 41 outliers final: 32 residues processed: 246 average time/residue: 0.0979 time to fit residues: 37.6415 Evaluate side-chains 245 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 110 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 420 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 307 ILE Chi-restraints excluded: chain B residue 310 TRP Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 210 LEU 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 270 MET Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 13 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115544 restraints weight = 26817.946| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.25 r_work: 0.3670 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14097 Z= 0.114 Angle : 0.643 13.172 19141 Z= 0.309 Chirality : 0.045 0.384 2164 Planarity : 0.004 0.050 2384 Dihedral : 4.957 53.826 1958 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.18 % Allowed : 21.30 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1662 helix: 1.26 (0.23), residues: 504 sheet: 0.44 (0.28), residues: 371 loop : -1.15 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 276 TYR 0.021 0.001 TYR D 325 PHE 0.018 0.001 PHE E 189 TRP 0.016 0.001 TRP D 267 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00254 (14089) covalent geometry : angle 0.62707 (19119) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.27472 ( 4) hydrogen bonds : bond 0.03615 ( 554) hydrogen bonds : angle 3.76471 ( 1926) link_NAG-ASN : bond 0.01057 ( 6) link_NAG-ASN : angle 4.63345 ( 18) ********************** 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 247 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.8101 (mm110) cc_final: 0.7679 (mm110) REVERT: D 210 GLN cc_start: 0.8694 (mp10) cc_final: 0.8117 (tt0) REVERT: D 300 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8426 (mmtm) REVERT: D 403 PHE cc_start: 0.6641 (m-10) cc_final: 0.5858 (m-80) REVERT: B 37 PHE cc_start: 0.9106 (t80) cc_final: 0.8640 (t80) REVERT: B 113 MET cc_start: 0.7942 (ppp) cc_final: 0.7393 (ppp) REVERT: B 135 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7207 (m) REVERT: B 168 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8167 (p0) REVERT: B 269 ASN cc_start: 0.7640 (m-40) cc_final: 0.7197 (t0) REVERT: B 270 MET cc_start: 0.7367 (mmm) cc_final: 0.7039 (ptp) REVERT: B 413 VAL cc_start: 0.7631 (t) cc_final: 0.7381 (p) REVERT: E 185 ASP cc_start: 0.8338 (p0) cc_final: 0.8121 (p0) REVERT: E 223 ASP cc_start: 0.6308 (t0) cc_final: 0.5860 (t0) REVERT: E 270 MET cc_start: 0.8471 (tmm) cc_final: 0.7363 (mmt) outliers start: 33 outliers final: 28 residues processed: 236 average time/residue: 0.0931 time to fit residues: 34.8481 Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 316 LEU 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 285 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 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN 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 201 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 GLN ** E 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.137994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113926 restraints weight = 26993.531| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.18 r_work: 0.3644 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14097 Z= 0.129 Angle : 0.667 13.059 19141 Z= 0.323 Chirality : 0.045 0.396 2164 Planarity : 0.004 0.054 2384 Dihedral : 5.021 54.110 1958 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.51 % Allowed : 21.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1662 helix: 1.27 (0.23), residues: 507 sheet: 0.45 (0.28), residues: 367 loop : -1.19 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.020 0.001 TYR D 325 PHE 0.021 0.001 PHE E 189 TRP 0.016 0.001 TRP E 284 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00297 (14089) covalent geometry : angle 0.65194 (19119) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.50458 ( 4) hydrogen bonds : bond 0.03692 ( 554) hydrogen bonds : angle 3.80284 ( 1926) link_NAG-ASN : bond 0.01043 ( 6) link_NAG-ASN : angle 4.64155 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.87 seconds wall clock time: 51 minutes 35.11 seconds (3095.11 seconds total)